Neandertal mtDNA (Query) compared with Human mtDNA (Sbjct):

 

To learn something about mitochondrial DNA (mtDNA):

 

http://cellbio.utmb.edu/cellbio/mitoch2.htm

 

http://www.neuro.wustl.edu/neuromuscular/mitosyn.html

 

http://www.cstl.nist.gov/div831/DNAtech/MitochondrialRes_Mut.html

 

 

24 differences including an INSERTION altering the reading frame (comparing a

fragment of 378 nucleotides)

AF011222

Krings,M., Stone,A., Schmitz,R.W., Krainitzki,H., Stoneking,M. and Paabo,S., 

Neandertal DNA sequences and the origin of modern humans, 

Cell 90 (1), 19-30 (1997)

Homo sapiens neanderthalensis mitochondrial D-loop hypervariable region 1

>gi|13272864|gb|AF346985.1|AF346985 Homo sapiens mitochondrion, complete genome.

Length = 16567

 Score =  509 bits (257), Expect = e-142

 Identities = 346/378 (91%), Gaps = 1/378 (0%)

 Strand = Plus / Plus

Query: 1     gttctttcatgggggagcagatttgggtaccacccaagtattgactcacccatcagcaac 60

             |||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||

Sbjct: 16021 gttctttcatggggaagcagatttgggtaccacccaagtattgactcacccatcaacaac 16080

Query: 61    cgctatgtatctcgtacattactgttagttaccatgaatattgtacagtaccataattac 120

             |||||||||| |||||||||||||  ||  |||||||||||||||||||||||||| |||

Sbjct: 16081 cgctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataaatac 16140

Query: 121   ttgactacctgcagtacataaaaacctaatccacatcaaacccccccccccatgcttaca 180

             ||||||||||| |||||||||||||  || |||||||||| |||  ||||||||||||||

Sbjct: 16141 ttgactacctgtagtacataaaaactcaacccacatcaaaaccctgcccccatgcttaca 16200

Query: 181   agcaagcacagcaatcaaccttcaactgtcatacatcaactacaactccaaagacgccct 240

             |||||| |||||||||||||||||||||||| ||||||||| ||||||||||| | ||| 

Sbjct: 16201 agcaagtacagcaatcaaccttcaactgtcacacatcaactgcaactccaaagccacccc 16260

Query: 241   tacacccactaggatatcaacaaacctacccacccttgacagtacatagcacataaagtc 300

             | |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||

Sbjct: 16261 t-cacccactaggataccaacaaacctacccacccttaacagtacatagcacataaagtc 16319

Query: 301   atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccccct 360

             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 16320 atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccccct 16379

Query: 361   cagataggggtcccttga 378

             ||||||||||||||||||

Sbjct: 16380 cagataggggtcccttga 16397

 

 

11 differences including 3 INSERTIONS (comparing a fragment of 345 nucleotides)

AF142095

Krings,M., Geisert,H., Schmitz,R.W., Krainitzki,H. and Paabo,S., 

DNA sequence of the mitochondrial hypervariable region II from the neandertal type specimen, 

Proc. Natl. Acad. Sci. U.S.A. 96 (10), 5581-5585 (1999).

Homo sapiens neanderthalensis mitochondrial control region, hypervariable region II.

>gi|10046763|emb|AJ297064.1|HSA297064 

Homo sapiens mitochondrial SDS-stable vimentin-bound DNA fragment 

HEF42VIM24. Length = 743

 Score =  593 bits (299), Expect = e-167

 Identities = 334/345 (96%), Gaps = 3/345 (0%)

 Strand = Plus / Plus

Query: 1   ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 60

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 57  ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 116

Query: 61  tgtcgcagtatctgtctttgattcctgccccattccattatttatcgcacctacgttcaa 120

           ||||||||||||||||||||||||||||| ||| ||||||||||||||||||||||||||

Sbjct: 117 tgtcgcagtatctgtctttgattcctgcctcatcccattatttatcgcacctacgttcaa 176

Query: 121 tattacaggcgagcatacttactaaagtgtgttaattaattaatgcttgtaggacataat 180

           |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 177 tattacaggcgaacatacttactaaagtgtgttaattaattaatgcttgtaggacataat 236

Query: 181 aataacgactaaatgtctgcacagctgctttccacacagacatcataacaaaaaatttcc 240

           |||||| | | |||||||||||||| ||||||||||||||||||||||||||||||||||

Sbjct: 237 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 296

Query: 241 accaaaccccctttcctcccccgcttctggccacagcacttaaacacatctctgccaaac 300

           |||||||||||   ||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 297 accaaaccccc---cctcccccgcttctggccacagcacttaaacacatctctgccaaac 353

Query: 301 cccaaaaacaaagaaccctaacaccagcctaaccagacttcaaat 345

           ||||||||||||||||||||||||||||||||||||| |||||||

Sbjct: 354 cccaaaaacaaagaaccctaacaccagcctaaccagatttcaaat 398

 

 

19 differences including one INSERTION altering the reading frame (comparing a fragment of 345 nucleotides)

AF254446  

Ovchinnikov,I.V., Gotherstrom,A., Romanova,G.P., Kharitonov,V.M., Liden,K. and Goodwin,W., 

Molecular analysis of Neanderthal DNA from the northern Caucasus, 

Nature 404 (6777), 490-493 (2000).

Homo sapiens neanderthalensis mitochondrial D-loop, hypervariable region I.

>gi|13272864|gb|AF346985.1|AF346985 Homo sapiens mitochondrion, 

complete genome. Length = 16567

 Score =  486 bits (245), Expect = e-135

 Identities = 318/345 (92%), Gaps = 1/345 (0%)

 Strand = Plus / Plus

Query: 1     ccaagtattgactcacccatcaacaaccgccatgtatttcgtacattactgccagccacc 60

             |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||

Sbjct: 16054 ccaagtattgactcacccatcaacaaccgctatgtatttcgtacattactgccagccacc 16113

Query: 61    atgaatattgtacagtaccataattacttgactacctgtaatacataaaaacctaatcca 120

             ||||||||||||||||||||||| |||||||||||||||| |||||||||||  || |||

Sbjct: 16114 atgaatattgtacagtaccataaatacttgactacctgtagtacataaaaactcaaccca 16173

Query: 121   catcaaccccccccccccatgcttacaagcaagcacagcaatcaaccttcaactgtcata 180

             ||||||  |||  |||||||||||||||||||| |||||||||||||||||||||||| |

Sbjct: 16174 catcaaaaccctgcccccatgcttacaagcaagtacagcaatcaaccttcaactgtcaca 16233

Query: 181   catcaactacaactccaaagacacccttacacccactaggatatcaacaaacctacccac 240

             |||||||| ||||||||||| ||||| | |||||||||||||| ||||||||||||||||

Sbjct: 16234 catcaactgcaactccaaagccacccct-cacccactaggataccaacaaacctacccac 16292

Query: 241   ccttgacagtacatagcacataaagtcatttaccgtacatagcacattatagtcaaatcc 300

             |||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||

Sbjct: 16293 ccttaacagtacatagcacataaagtcatttaccgtacatagcacattacagtcaaatcc 16352

Query: 301   cttctcgcccccatggatgacccccctcagataggggtcccttga 345

             |||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 16353 cttctcgcccccatggatgacccccctcagataggggtcccttga 16397

 

 

19 differences including one INSERTION altering the reading frame (comparing a fragment of 357 nucleotides)

AF282971

Krings,M., Capelli,C., Tschentscher,F., Geisert,H., Meyer,S., von Haeseler,A., Grossschmidt,K., Possnert,G., 

Paunovic,M. and Paabo,S., A view of neandertal genetic diversity, Nat. Genet. 

26 (2), 144-146 (2000).

Homo sapiens neanderthalensis mitochondrial hypervariable region I sequence.

>gi|13272864|gb|AF346985.1|AF346985 Homo sapiens mitochondrion, 

complete genome. Length = 16567

 Score =  502 bits (253), Expect = e-140

 Identities = 329/357 (92%), Gaps = 1/357 (0%)

 Strand = Plus / Plus

Query: 1     gttctttcatgggggagcagatttgggtaccacccaagtattgactcacccatcagcaac 60

             |||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||

Sbjct: 16021 gttctttcatggggaagcagatttgggtaccacccaagtattgactcacccatcaacaac 16080

Query: 61    cgctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataattac 120

             |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||

Sbjct: 16081 cgctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataaatac 16140

Query: 121   ttgactacctgcagtacataaaaacctaatccacatcaaccccccccccccatgcttaca 180

             ||||||||||| |||||||||||||  || |||||||||  |||  ||||||||||||||

Sbjct: 16141 ttgactacctgtagtacataaaaactcaacccacatcaaaaccctgcccccatgcttaca 16200

Query: 181   agcaagcacagcaatcaaccttcaactgtcatacatcaactacaactccaaagacgccct 240

             |||||| |||||||||||||||||||||||| ||||||||| ||||||||||| | ||| 

Sbjct: 16201 agcaagtacagcaatcaaccttcaactgtcacacatcaactgcaactccaaagccacccc 16260

Query: 241   tacacccactaggatatcaacaaacctacccacccttgacagtacatagcacataaagtc 300

             | |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||

Sbjct: 16261 t-cacccactaggataccaacaaacctacccacccttaacagtacatagcacataaagtc 16319

Query: 301   atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccc 357

             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 16320 atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccc 16376

 

 

9 differences including a DELETION altering the reading frame (comparing a fragment of 288 nucleotides)

AF282972  

Krings,M., Capelli,C., Tschentscher,F., Geisert,H., Meyer,S., von Haeseler,A., Grossschmidt,K., Possnert,G., 

Paunovic,M. and Paabo,S., A view of neandertal genetic diversity, Nat. Genet. 26 (2), 144-146 (2000).

Homo sapiens neanderthalensis mitochondrial hypervariable region II sequence. 

>gi|13272794|gb|AF346980.1|AF346980 Homo sapiens mitochondrion, 

complete genome. Length = 16570

 Score =  494 bits (249), Expect = e-137

 Identities = 280/289 (96%), Gaps = 1/289 (0%)

 Strand = Plus / Plus

Query: 1   ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 60

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 57  ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 116

Query: 61  tgtcgcagtatctgtctttgattcctgccccattccattatttatcgcacctacgttcaa 120

           ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||

Sbjct: 117 tgtcgcagtatctgtctttgattcctgcctcattctattatttatcgcacctacgttcaa 176

Query: 121 tattacaggcgagcatacttactgaagtgtgttaattaattaatgcttgtaggacataat 180

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 177 tattacaggcgagcatacttactgaagtgtgttaattaattaatgcttgtaggacataat 236

Query: 181 aataacgactaaatgtctgcacagctgctttccacacagacatcataacaaaaaatttcc 240

           |||||| | | |||||||||||||| ||||||||||||||||||||||||||||||||||

Sbjct: 237 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 296

Query: 241 accaaacctccccct-cccccgcttctggccacagcacttaaatacatc 288

           |||||||| |||||| ||||||||||||||||||||||||||| |||||

Sbjct: 297 accaaacccccccctccccccgcttctggccacagcacttaaacacatc 345

18 Differences including one INSERTION altering the reading frame (comparing a 

fragment of 357 nucleotides)

AY149291

Schmitz,R.W., Serre,D., Bonani,G., Feine,S., Hillgruber,F., Krainitzki,H., 

Paabo,S. and Smith,F.H., The Neandertal type site revisited: 

interdisciplinary investigations of skeletal remains from the Neander 

Valley, Germany, Proc. Natl. Acad. Sci. U.S.A. 99 (20), 13342-13347 (2002).

>gi|13272864|gb|AF346985.1|AF346985 Homo sapiens mitochondrion, 

complete genome. Length = 16567

 Score =  509 bits (257), Expect = e-142

 Identities = 330/357 (92%), Gaps = 1/357 (0%)

 Strand = Plus / Plus

Query: 1     gttctttcatgggggagcagatttgggtaccacccaagtattgactcacccatcagcaac 60

             |||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||||

Sbjct: 16021 gttctttcatggggaagcagatttgggtaccacccaagtattgactcacccatcaacaac 16080

Query: 61    cgctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataattac 120

             |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||

Sbjct: 16081 cgctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataaatac 16140

Query: 121   ttgactacctgcagtacataaaaacctaatccacatcaaccccccccccccatgcttaca 180

             ||||||||||| |||||||||||||  || |||||||||  |||  ||||||||||||||

Sbjct: 16141 ttgactacctgtagtacataaaaactcaacccacatcaaaaccctgcccccatgcttaca 16200

Query: 181   agcaagcacagcaatcaaccttcaactgtcatacatcaactacaactccaaagacaccct 240

             |||||| |||||||||||||||||||||||| ||||||||| ||||||||||| ||||| 

Sbjct: 16201 agcaagtacagcaatcaaccttcaactgtcacacatcaactgcaactccaaagccacccc 16260

Query: 241   tacacccactaggatatcaacaaacctacccacccttgacagtacatagcacataaagtc 300

             | |||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||

Sbjct: 16261 t-cacccactaggataccaacaaacctacccacccttaacagtacatagcacataaagtc 16319

Query: 301   atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccc 357

             |||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 16320 atttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccc 16376

////////////////////////////////

Human mtDNA (Query) compared with Human mtDNA (Sbjct):

 

5 differences NO INSERTIONS or DELETIONS

Comparing the AF346985 (a fragment 16567 long)

>gi|1946433|gb|U93974.1|HSU93974 Human isolate 128KT hypervariable region I, mitochondrial sequence. Length = 360

 Score =  674 bits (340), Expect = 0.0

 Identities = 355/360 (98%)

 Strand = Plus / Plus

Query: 2   ttctttcatggggaagcagatttgggtaccacccaagtattgactcacccatcaacaacc 61

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 1   ttctttcatggggaagcagatttgggtaccacccaagtattgactcacccatcaacaacc 60

Query: 62  gctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataaatact 121

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 61  gctatgtatttcgtacattactgccagccaccatgaatattgtacagtaccataaatact 120

Query: 122 tgactacctgtagtacataaaaactcaacccacatcaaaaccctgcccccatgcttacaa 181

           |||||||||||||||||||||||| ||||||||||||||||||  |||||||||||||||

Sbjct: 121 tgactacctgtagtacataaaaacccaacccacatcaaaaccccacccccatgcttacaa 180

Query: 182 gcaagtacagcaatcaaccttcaactgtcacacatcaactgcaactccaaagccacccct 241

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 181 gcaagtacagcaatcaaccttcaactgtcacacatcaactgcaactccaaagccacccct 240

Query: 242 cacccactaggataccaacaaacctacccacccttaacagtacatagcacataaagtcat 301

           ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||

Sbjct: 241 cacccactaggataccaacaaacctgcccacccttaacagtacatagcacataaagtcat 300

Query: 302 ttaccgtacatagcacattacagtcaaatcccttctcgcccccatggatgacccccctca 361

           |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||

Sbjct: 301 ttaccgtacatagcacattacagtcaaatcccttctcgtccccatggatgacccccctca 360

1 difference NO INSERTIONS or DELETIONS

Comparing HSA297064 (a fragment 743 bases long)

>gi|2804659|gb|U95679.1|HSU95679 Homo sapiens sample EW6 mitochondrial 

control region II, partial sequence Length = 344

 Score =  480 bits (242), Expect = e-133

 Identities = 245/246 (99%)

 Strand = Plus / Plus

Query: 1   ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 60

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 19  ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 78

Query: 61  tgtcgcagtatctgtctttgattcctgcctcatcccattatttatcgcacctacgttcaa 120

           ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||

Sbjct: 79  tgtcgcagtatctgtctttgattcctgcctcatcctattatttatcgcacctacgttcaa 138

Query: 121 tattacaggcgaacatacttactaaagtgtgttaattaattaatgcttgtaggacataat 180

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 139 tattacaggcgaacatacttactaaagtgtgttaattaattaatgcttgtaggacataat 198

Query: 181 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 240

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 199 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 258

Query: 241 accaaa 246

           ||||||

Sbjct: 259 accaaa 264

Query: 260 gcttctggccacagcacttaaacacatctctgccaaaccccaaaaacaaagaaccctaac 319

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 280 gcttctggccacagcacttaaacacatctctgccaaaccccaaaaacaaagaaccctaac 339

Query: 320 accag 324

           |||||

Sbjct: 340 accag 344

3 differences NO INSERTIONS or DELETIONS

comparing with AF346980 (a fragment 16570 bases long)

>gi|1235613|gb|L39332.1|HUMMTFRAJ Homo sapiens mitochondrial control 

region II, sample NG11. Length = 344

 Score =  464 bits (234), Expect = e-128

 Identities = 243/246 (98%)

 Strand = Plus / Plus

Query: 1   ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 60

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 19  ttttcgtctggggggtgtgcacgcgatagcattgcgagacgctggagccggagcacccta 78

Query: 61  tgtcgcagtatctgtctttgattcctgcctcattctattatttatcgcacctacgttcaa 120

           ||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||

Sbjct: 79  tgtcgcagtatctgtctttgattcctgcctcatcctattatttatcgcacctacgttcaa 138

Query: 121 tattacaggcgagcatacttactgaagtgtgttaattaattaatgcttgtaggacataat 180

           |||||||||||| |||||||||| ||||||||||||||||||||||||||||||||||||

Sbjct: 139 tattacaggcgaacatacttactaaagtgtgttaattaattaatgcttgtaggacataat 198

Query: 181 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 240

           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct: 199 aataacaattgaatgtctgcacagccgctttccacacagacatcataacaaaaaatttcc 258

Query: 241 accaaa 246

           ||||||

Sbjct: 259 accaaa 264

Query: 262 gcttctggccacagcacttaaacacatc 289

           ||||||||||||||||||||||||||||

Sbjct: 280 gcttctggccacagcacttaaacacatc 307