CYTOCHROME C1 *This is the original AA sequence GELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLIGVTHTEAE 60 AKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYAR 120 HGGEDYVFSLLTGYCDPPAGVVVREGLHYNPYFPGQAIGMAPPIYNEILEYDDGTPATMS 180 QIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLTSLLYYMKRHKWSVLKSRKMAYRPP 240 K 241 * 2 matching DNA strands found in Genebank >gi|28175292|gb|BC045127.1| Xenopus laevis, Similar to cytochrome c-1, clone MGC:53391 IMAGE:5571517, mRNA, complete cds Length = 1282 Score = 399 bits (1025), Expect = e-109 Identities = 180/240 (75%), Positives = 202/240 (84%) Frame = +3 1 gacgtaaagc cggctggaag gtggggatca agcttcctgt gtgagagaga aagatggcgg 61 cggcgtgcct ggttttgcgg aggtcgctgc ggggagcagt actgcaaggg ggacgggtgg 121 cctggccggt ggctcctcag gccaacatgt cgttctcggc tctgtcccgg ggcaggaagg 181 tggctctctc cacattgggt attttggtcg ctggaggctc cggtttggca tttgctctcc 241 accaatcagt gaaagccagt gaattagagc tgcacccgcc ctcctaccca tggagccaca 301 gcggatttct ctcctctttg gatcatggca gcatccgccg tggttaccag gtgtacaagc 361 aggtgtgtgc cgcgtgtcac agtatggaat acttggcctt taggaatctc atcggcgtct 421 cccacactga agcagaagcc aaagctctgg cggaggagtt tgagattcag gatgggccgg 481 atgagaatgg ggagatgttc cttcgccccg ggaaactgtc cgattatttc cccaaaccgt 541 atgccaacga ggaggcggcc agagcgtcca acaatggggc cctgccccca gatctcagct 601 acatcgccaa cgccaggcac gggggcgagg attacatctt ctctcttctg actggttact 661 gcgaccctcc tgccggcgtc actttaagag aaggacttta ctacaacccc tacttcccag 721 gccaggccgt cgggatggca ccccctattt ataacgaggt tttggaatat gaggatggga 781 caccggccac catgtctcag gttgctaagg acgtgtccac attcctgcgt tgggcttcag 841 aaccagaaca cgaccatcgc aagcgcatgg gccttaaagt gctgatgatc tcctccatcc 901 tcatccctct catctactac atgaagagac acagatggag tgttctgaag tccaggaaga 961 tcgcctacag accccccaag taacggattg tgcccccctg tgtatcagtg gcctgggcta 1021 gcggctgcaa tggaggagtt gcccaaacac acggcccctt tgctcctcgg agcaggaaca 1081 tcacagacgc tgcgtccgta gctccatctt tgcgtttttt ttttatgggt ttttttttgt 1141 cgtagggaat ttttcttctc tgttaatgtc cgaaaagaag ccccccgagg agataaaggg 1201 acccgtgcaa agaaaacatt gtcttttgtc cattacttcc cttaaattaa acaaaaatag 1261 atcttttaaa aaaaaaaaaa aa >gi|13542840|gb|BC005620.1| Mus musculus cytochrome c-1, mRNA (cDNA clone MGC:11682 IMAGE:3711323), complete cds Length = 1204 Score = 390 bits (1003), Expect = e-107 Identities = 178/240 (74%), Positives = 202/240 (84%) Frame = +2 1 ggccgcacta aagggggccg acatggcggc ggcggcggct tcgcttcgcc ggacggtact 61 gggcccgcgg ggcgtggggc ttccaggtgc aagtgctccg ggtctgctgg gcggcgcgcg 121 gtcccggcag cttccattgc ggacaccgca ggcagtgtcc ttgtcctcga agtctggccc 181 ttctcgaggc cgaaaggtga tgctgtcagc gttgggcatg ctggccgcgg ggggtgcagg 241 gctagctgtg gcccttcatt ctgccgtgag tgccagtgac ctggagctgc acccccccag 301 ctacccatgg tctcatcgtg gcctcctctc ctccttggac cacaccagca ttcggagggg 361 tttccaggta tacaagcagg tgtgctcttc ctgccacagc atggattatg tggcgtaccg 421 ccacctggtg ggagtgtgct acacggagga agaagccaag gcgctggctg aggaggtgga 481 ggtccaggat ggccctaatg atgatgggga gatgttcatg cggccaggga agttgtctga 541 ctattttcca aaaccatacc ctaaccctga ggctgcaaga gctgctaaca atggagcttt 601 accccctgac ctcagctaca tcgttcgagc taggcatggt ggtgaggact acgtattttc 661 cctgctcact ggctactgtg agccccccac tggggtgtca ttgcgagaag gcctctattt 721 caacccttac tttcccggcc aggccattgg catggctcct cccatctaca cagaagtctt 781 ggagtatgat gatggcaccc cagctaccat gtcacaagta gctaaggatg tcgccacctt 841 ccttcgctgg gcatcagaac cagagcatga ccatcgaaaa cgcatgggtc tcaagatgtt 901 gttgatgatg ggcctgctgc tgcccctgac ctatgccatg aagcggcata agtggtcagt 961 cctgaagagt cgaaagctgg cttatcggcc acccaagtga ccctgttcag tatctgcttg 1021 tcatcttgcc agaacaagct ctcagcagcc caggaacagt ccatggcctt ctcaggcctg 1081 gcccttttca tcagatacaa gggccaggag accagactct tgcttctgat cttccttcag 1141 ccctcagtgt gggaataaat taagtttctc aacataaaaa aaaaaaaaaa aaaaaaaaaa 1201 aaaa * using the first DNA strand (>gi|28175292|gb|BC045127.1| Xenopus laevis, Similar to cytochrome c-1, clone MGC:53391) and searched on U of Delaware blast program and found the following 2 strands http://www.chickest.udel.edu/public_php/getSequence.php?seqId=78275&type=standard >pgl1n.pk013.f13 1 CGTCGTTCTC GGCTCAGCCC CGGGGCCGCC TGAGGGTTCT GGCGGCTCTG GGAGCTCTGA 60 61 CGGCGGGGGG GGCGGCGGCG GCGGTCGTAG CGCTGAAGGC GGCGGTGGAC GCGGGGGAGT 120 121 TGGAGCTGCA CCCCCCCGCC TTCCCGTGGA GCCACGGGGG GCCGCTCTCT GCGTTGGACC 180 181 ACAGCAGTGT GCGCCGTGGC TTCCAGGTGT ACAAGCAGGT GTGCTCCGCG TGCCACAGCA 240 241 TGGACTACGT CGCCTTCAGG AACCTCATTG GGGTCACCCA CACCGAGGCT GAGGCCAAAG 300 301 CGTTGGCCGA GGAGGTGGAG GTTCAGGACG GCCCGGATGA GAACGGGGAG CTGTTTATGC 360 361 GGCCCGGGAA GATCTCGGAT TACTTCCCCA AACCGTACCC CAACCCCGAG GCTGCGCGCG 420 421 CCGACAACAA CGGGGCGCTG CCCCCCGACC TCAGCTACAT CGTCTATGCC AGACACGNNN 480 481 NG http://www.chickest.udel.edu/public_php/getSequence.php?seqId=73731&type=standard >pgp1n.pk001.b7 Length: 679 Standard View 1 CGGCGGCGTC CCCGCGACCT CAGCGCTGCG GCGATGGCGG CGGCGGTGGC TGCGGGGCGG 60 61 CGTTTCCCTT TACGGCCTTG CGGGCGTCTC CTGCTCAGCC CGAGGCCTCG GCCGGCTCCG 120 121 CAGGGGGCCC GTCCGGCGTC GTTCTCGGCT CAGCCCCGGG GCCGCCTGAG GGTTCTGGCG 180 181 GCTCTGGGAG CTCTGACGGC GGGGGGGGCG GCGGCGGCGG TCGTAGCGCT GAAGGCGGCG 240 241 GTGGACGCGG GGGAGTTGGA GCTGCACCCC CCCGCCTTCC CGTGGAGCCA CGGGGGGCCG 300 301 CTCTCTGCGT TGGACCACAG CAGTGTGCGC CGTGGCTTCC AGGTGTACAA GCAGGTGTGC 360 361 TCCGCGTGCC ACAGCATGGA CTACGTCGCC TTCAGGAACC TCATTGGGGT CACCCACACC 420 421 GAGGCTGAGG CCAAAGCGTT GGCCGAGGAG GTGGAGGTTC AGGACGGCCC GGATGAGAAC 480 481 GGGGAGCTGT TTATGCGGCC CGGGAAGATC TCGGATTACT TCCCCAAACC GTACCCCAAC 540 541 CCCGNNNCTG CGCGCGCCNN NAACAACGGG GCGCTGCCCC CCGACCTCAG CTACATCGTC 600 601 AATGCCAGAC ACGNNNGGGA GGATTACGTC TTCTCGTTGC TGACNNNNTA CTNNNANCCC 660 661 CCGCGGGCGT TGTGGTGCG Together, the sequence is aligned CLUSTAL W (1.8) multiple sequence alignment pgl1npk013f13 ------------------------------------------------------------ pgp1npk001b7 CGGCGGCGTCCCCGCGACCTCAGCGCTGCGGCGATGGCGGCGGCGGTGGCTGCGGGGCGG pgl1npk013f13 ------------------------------------------------------------ pgp1npk001b7 CGTTTCCCTTTACGGCCTTGCGGGCGTCTCCTGCTCAGCCCGAGGCCTCGGCCGGCTCCG pgl1npk013f13 ----------------CGTCGTTCTCGGCTCAGCCCCGGGGCCGCCTGAGGGTTCTGGCG pgp1npk001b7 CAGGGGGCCCGTCCGGCGTCGTTCTCGGCTCAGCCCCGGGGCCGCCTGAGGGTTCTGGCG ******************************************** pgl1npk013f13 GCTCTGGGAGCTCTGACGGCGGGGGGGGCGGCGGCGGCGGTCGTAGCGCTGAAGGCGGCG pgp1npk001b7 GCTCTGGGAGCTCTGACGGCGGGGGGGGCGGCGGCGGCGGTCGTAGCGCTGAAGGCGGCG ************************************************************ pgl1npk013f13 GTGGACGCGGGGGAGTTGGAGCTGCACCCCCCCGCCTTCCCGTGGAGCCACGGGGGGCCG pgp1npk001b7 GTGGACGCGGGGGAGTTGGAGCTGCACCCCCCCGCCTTCCCGTGGAGCCACGGGGGGCCG ************************************************************ pgl1npk013f13 CTCTCTGCGTTGGACCACAGCAGTGTGCGCCGTGGCTTCCAGGTGTACAAGCAGGTGTGC pgp1npk001b7 CTCTCTGCGTTGGACCACAGCAGTGTGCGCCGTGGCTTCCAGGTGTACAAGCAGGTGTGC ************************************************************ pgl1npk013f13 TCCGCGTGCCACAGCATGGACTACGTCGCCTTCAGGAACCTCATTGGGGTCACCCACACC pgp1npk001b7 TCCGCGTGCCACAGCATGGACTACGTCGCCTTCAGGAACCTCATTGGGGTCACCCACACC ************************************************************ pgl1npk013f13 GAGGCTGAGGCCAAAGCGTTGGCCGAGGAGGTGGAGGTTCAGGACGGCCCGGATGAGAAC pgp1npk001b7 GAGGCTGAGGCCAAAGCGTTGGCCGAGGAGGTGGAGGTTCAGGACGGCCCGGATGAGAAC ************************************************************ pgl1npk013f13 GGGGAGCTGTTTATGCGGCCCGGGAAGATCTCGGATTACTTCCCCAAACCGTACCCCAAC pgp1npk001b7 GGGGAGCTGTTTATGCGGCCCGGGAAGATCTCGGATTACTTCCCCAAACCGTACCCCAAC ************************************************************ pgl1npk013f13 CCCGAGGCTGCGCGCGCCGACAACAACGGGGCGCTGCCCCCCGACCTCAGCTACATCGTC pgp1npk001b7 CCCGNNNCTGCGCGCGCCNNNAACAACGGGGCGCTGCCCCCCGACCTCAGCTACATCGTC **** *********** *************************************** pgl1npk013f13 TATGCCAGACACGNNNNG------------------------------------------ pgp1npk001b7 AATGCCAGACACGNNNGGGAGGATTACGTCTTCTCGTTGCTGACNNNNTACTNNNANCCC *************** * pgl1npk013f13 ------------------- pgp1npk001b7 CCGCGGGCGTTGTGGTGCG Then using 6frame, AA sequence is translated from DNA: GELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLIGVTHTEAE AKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYAR HGGEDYVFSLLTGYCDPPAGVVVREGLHYNPYFPGQAIGMAPPIYNEILEYDDGTPATMS QIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLTSLLYYMKRHKWSVLKSRKMAYRPP K >pgl1n.pk013.f13 Frame 2 SFSAQPRGRLRVLAALGALTAGGAAAAVVALKAAVDAGELELHPPAFPWSHGGPLSALDH SSVRRGFQVYKQVCSACHSMDYVAFRNLIGVTHTEAEAKALAEEVEVQDGPDENGELFMR PGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYARHXX >pgp1n.pk001.b7 Frame 0 RRRPRDLSAAAMAAAVAAGRRFPLRPCGRLLLSPRPRPAPQGARPASFSAQPRGRLRVLA ALGALTAGGAAAAVVALKAAVDAGELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVC SACHSMDYVAFRNLIGVTHTEAEAKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPN PXXARAXNNGALPPDLSYIVNARHXXEDYVFSLLXXYXXPPRALWC Alignment betweeen original and pgl1n.pk013.f13 CLUSTAL W (1.8) multiple sequence alignment GELELHPPAFPWSHGGPLSALDHSSVRRGF -------------------------------------AKALAEEVEVQDG SFSAQPRGRLRVLAALGALTAGGAAAAVVA SSVRRGFQVYKQVCSACHSMDYVAFRNLIGVTHTEAEAKALAEEVEVQDG ************* GELELHPPAFPWSHGGPLSALDHSSVRRGF PDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYARHGG SFSAQPRGRLRVLAALGALTAGGAAAAVVA PDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYARHXX ************************************************ GELELHPPAFPWSHGGPLSALDHSSVRRGF EDYVFSLLTGYCDPPAGVVVREGLHYNPYFPGQAIGMAPPIYNEILEYDD SFSAQPRGRLRVLAALGALTAGGAAAAVVA -------------------------------------------------- GELELHPPAFPWSHGGPLSALDHSSVRRGF GTPATMSQIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLTSLLYYMK SFSAQPRGRLRVLAALGALTAGGAAAAVVA -------------------------------------------------- GELELHPPAFPWSHGGPLSALDHSSVRRGF RHKWSVLKSRKMAYRPPK SFSAQPRGRLRVLAALGALTAGGAAAAVVA ------------------ Alignment betweeen original and pgp1n.pk001.b7 LUSTAL W (1.8) multiple sequence alignment GELELHPPAFPWSHGGPLSALDHSSVRRGF ------AKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPNPEAARAD RRRPRDLSAAAMAAAVAAGRRFPLRPCGRL ALGALTAGGAAAAVVALKAAVDAGELELHP----PAFPWSHGGPLSALDH * . * * . ... : *** ::* ** .: .* :* . GELELHPPAFPWSHGGPLSALDHSSVRRGF NNGALPPDLSYIVYARHGGEDYVFSLLTGYCDPPAGVVVREGLHYNPYFP RRRPRDLSAAAMAAAVAAGRRFPLRPCGRL S---------S---VRRGFQ--VYKQVCSACHSMDYVAFRN-LIGVTHTE . .*:* : *:. : . *.. *..*: * .: GELELHPPAFPWSHGGPLSALDHSSVRRGF GQAIGMAPPIYNEILEYDDGTPATMSQIAKDVCTFLRWAAEPEHDQRKRM RRRPRDLSAAAMAAAVAAGRRFPLRPCGRL AEAKALAEEV--EVQDGPDENGELFMRPGKISDYFPKPYPNPXXARAXNN .:* .:* : *: : * . : : .* * : .:* : . GELELHPPAFPWSHGGPLSALDHSSVRRGF GLKMLLISALLTSLLYYMKRHKWSVLKSRKMAYRPPK- RRRPRDLSAAAMAAAVAAGRRFPLRPCGRL GALPPDLSYIVNARHX-XEDYVFSLLXXYXXPPRALWC * :* ::.: : : :*:* . *. alignment between pgp1n.pk001.b7 and pgl1n.pk013.f13 CLUSTAL W (1.8) multiple sequence alignment pgl1npk013f13 ----------------------------------------------SFSAQPRGRLRVLA pgp1npk001b7 RRRPRDLSAAAMAAAVAAGRRFPLRPCGRLLLSPRPRPAPQGARPASFSAQPRGRLRVLA ************** pgl1npk013f13 ALGALTAGGAAAAVVALKAAVDAGELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVC pgp1npk001b7 ALGALTAGGAAAAVVALKAAVDAGELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVC ************************************************************ pgl1npk013f13 SACHSMDYVAFRNLIGVTHTEAEAKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPN pgp1npk001b7 SACHSMDYVAFRNLIGVTHTEAEAKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPN ************************************************************ pgl1npk013f13 PEAARADNNGALPPDLSYIVYARHXX-------------------- pgp1npk001b7 PXXARAXNNGALPPDLSYIVNARHXXEDYVFSLLXXYXXPPRALWC * *** ************* *****