RetrogeneDB ID: retro_btau_1380

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:41827702..41829357(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSBTAG00000002507
• Aliases: None
• Description: ATP synthase subunit alpha, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_777109]

Sequence

>retro_btau_1380
ATGCTGTCCGTGCTCATGGCCATGGCCGTACCCACGCCTTCCCTTTGTGAGCCAGGCTGGTCTCCAAAAATGCTTTGGGA
TCATCCTTCATTGCTGCAAGGAACCTCCATGCCTCTAACTCTTGTCTTCAGAAGACTGGCACTGCTGAGGTGTCCTCTGT
TCTTGAAGAGCGTATTCTTGGAGCTGATACCTCTGTTAACCTTGAAGAGACTGGGCATGTTTTAAGTATTGGTGATTATA
TTGCCCGGGTATTTGGGCTAAGAAATGTTCAAGCAGAAGAAATGGTAGAATTTTCTTTAGGTTTAAAGGGTATGTCTCTG
AACTTGGAGTCTGACAACGTTGGTGTTGTTGTGTTTGGAAGTGATAAACTAATTAAGAAAGGAGATATTGTGAAGAGAAC
TGAAGCTATTGTAGATGTTCCAGTCAGTGAGGAGCTGCTGGGTCATGTAGTCTATGCCCTTGGTAATGCCACTGATGGAA
AGTGTCCAATTGGTTCCAAGGCCCGAAGACGAGTTGGCTTGAAAGCCCCTGGGGTCATTCCTCGAATCTCTGTGCGGGAA
CTAACACAAACTGGCATTAAGGCTGTGGACAGCTTGGTGCTGATTGGTCATGGTCAGTGTGATCTGGTTATTGGTGACCG
ATAGACTGGCAAAACACCAATTGCCAGAAACATCATTAACCAGAAATGATTCAATGATGGAACTGATGAAAAGAAGAAGC
TGTACTGTATCCATGTTGCTATTGGTCAAAAGAGATCCACTGTTGCCCAGTTGGTGAAGAGACTTACAGATGCAGATGCC
ATGAAGTATACTATTGTGGTTTCAGATACTGCTTCAGATGCTGCCCCACTTTAGTACCTGGCTCCTTACTCTGGATGTTC
AACGGGAGAATATTTTAGGGATAATGGCAAACATGCTTTGATTGTTTATGATGACTTATCCAAACAGGCAGTTGCTTATC
ATCAGATATCTATGGTGCTCTGCCCACCGCCCAGTCGTGAGGCCTGTCCTCGTGATGTGTTCTACCTGCACTCCCATATA
CTGGAGAGAGCAGCTAAAATGAACGATGCTTTTGATGGTGGCTCGTTAACTGCTCTACCACTCACAGAAGCACAAGCTGG
TGATGTGTCTGCTTACATTCCAACAAATGTCATTTCCATCACTGACAGACAGATCTTCTTGGAAACAGAGTTGTTCTACA
AAGGTATCCTCCCTGCCATTAATGTTGGTTTGTCTGTGTCCCATGTCAGATCTGCTGCCCAAACCAGGGTCATGAAACAG
GTGGCAGGTGCCATGAAACTGGAGTTGGCTCAGAATCGTGAGGTTGCTGCTTTTGCCTAGTTCGATTCTGACCTTGATGC
TGCCACTCAACAACTCTTGAGTCATGGTGTGCATTTCACTGAGCTGCTGAAGCAAGGACAATATTCTCCTATGGCTATTG
AAGAGCAAGTGGCTGTTATCTATGCGGGTGTCAGGGAGTATCTTGACAAGCTGGAGCCCAGCAAGATCACAAAATTTGAG
AATGCTTTCTTGCCTCATGTTATCAGCCAACATCAAGCCCTGTTGGGCAAAACCAGGACCAATGGAAAGTTCTCAGAAGA
GACAGATGCAAAGCTGAAAGAGATTATAACAAACTTCTTGGCTGGATTTGAAGCT

Alignment

ORF - retro_btau_1380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSVRVAAAV-ARALPRRAGLVSKNALGSSFIAARNLHASNSRLQKTGTAEVSSILEERILGADTSVDLE
          MLSV..A.AV...A.P..A.LVSKNALGSSFIAARNLHASNS.LQKTGTAEVSS.LEERILGADTSV.LE
Retrocopy MLSVLMAMAV<THAFPL*ARLVSKNALGSSFIAARNLHASNSCLQKTGTAEVSSVLEERILGADTSVNLE

Parental  ETGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVD
          ETG.VLSIGD.IARV.GLRNVQAEEMVEFS.GLKGMSLNLE.DNVGVVVFG.DKLIK.GDIVKRT.AIVD
Retrocopy ETGHVLSIGDYIARVFGLRNVQAEEMVEFSLGLKGMSLNLESDNVGVVVFGSDKLIKKGDIVKRTEAIVD

Parental  VPVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQREL
          VPV.EELLG.VV.ALGNA.DGK.PIGSKARRRVGLKAPG.IPRISVRE..QTGIKAVDSLV.IG.GQ..L
Retrocopy VPVSEELLGHVVYALGNATDGKCPIGSKARRRVGLKAPGVIPRISVRELTQTGIKAVDSLVLIGHGQCDL

Parental  IIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATA
          .IGDR.TGKT.IA...IINQK.FNDGTDEKKKLYCI.VAIGQKRSTVAQLVKRLTDADAMKYTIVVS.TA
Retrocopy VIGDR*TGKTPIARN-IINQK*FNDGTDEKKKLYCIHVAIGQKRSTVAQLVKRLTDADAMKYTIVVSDTA

Parental  SDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLL
          SDAAPL.YLAPYSGCS.GEYFRDNGKHALI.YDDLSKQAVAY.Q.S..L..PP.REA.P.DVFYLHS..L
Retrocopy SDAAPL*YLAPYSGCSTGEYFRDNGKHALIVYDDLSKQAVAYHQISMVLCPPPSREACPRDVFYLHSHIL

Parental  ERAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGS
          ERAAKMNDAF.GGSLTALP..E.QAGDVSAYIPTNVISITD.QIFLETELFYKGI.PAINVGLSVS.V.S
Retrocopy ERAAKMNDAFDGGSLTALPLTEAQAGDVSAYIPTNVISITDRQIFLETELFYKGILPAINVGLSVSHVRS

Parental  AAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIY
          AAQTR.MKQVAG.MKLELAQ.REVAAFA.F.SDLDAATQQLLS.GV..TELLKQGQYSPMAIEEQVAVIY
Retrocopy AAQTRVMKQVAGAMKLELAQNREVAAFA*FDSDLDAATQQLLSHGVHFTELLKQGQYSPMAIEEQVAVIY

Parental  AGVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA
          AGVR.YLDKLEPSKITKFENAFL.HVISQHQALLGK.RT.GK.SEE.DAKLKEI.TNFLAGFEA
Retrocopy AGVREYLDKLEPSKITKFENAFLPHVISQHQALLGKTRTNGKFSEETDAKLKEIITNFLAGFEA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
ERP005899_liver	0.00 RPM	168.20 RPM
ERP005899_muscle	0.11 RPM	989.64 RPM
SRP017611_brain	0.00 RPM	344.01 RPM
SRP017611_kidney	0.06 RPM	820.02 RPM
SRP017611_liver	0.00 RPM	219.35 RPM
SRP030211_testis	0.03 RPM	253.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1380 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1380 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380 , retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,