RetrogeneDB ID: retro_btau_1426

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 5:54107100..54108759(-)
• Located in intron of: ENSBTAG00000021287

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_1426
ATGCTGTCCGTGCGCGTCGCCGTGGCCATGGCCTGCGCCCTCCCTCGGCAAGTGGGGCTGGTCTCCAAAAATGCTTTGGG
ATCATCCTTCATTGCTGCAAGGAACCTGCATGCCTCTAACTCTTGTCTGCAGAAGACAGGCACTGCTGAGGTGTCCTCTA
TTCTCGAAGAGCGTATTCTTGGAGCTGATACCTCTGTTGACCTTGAAGAGACTGGGCGTGTTTTAAGTATTGGTGATGGT
ATTGCTCGGGTACATGGGTTAAGAGATGTTCAAGCAGAAGAAATGGTAGAGTTTTCTTCAGGTTTAAAGGGTATGTCTCT
GAACTTGGAGCCTGACAATGTTGGTGTTGTCGTGTTTGGAAATGATAAACTTATTAAGGAAGGAGATATTGTGAAGAGAA
CTGGGGCTATTGTAGATGTTCCAGTTGGCGAGGAGCTGCTGGGTCGTGTAGTCGATGCCCTCGGTAATGCCATTGATGGA
AAGAGTCCAATTGGTTCCAAGGCCCGAAGATGAGTTGGCTTGAAAGCCCCTGGGATCATTCCTCGAATCTCTGTGACGGA
ACCAATGCAAACTGGCATTAAGGCTGTGGATAGCTTGGTGCCGATTGGTCGTGGTCAGCGTGAGCTGATTATTGGTGACC
GACAGACTGGCAAAATGTCAATTGCAATTGACACAATCATTAACCAGAAACGATTCAATGATGGAACTGATGAAAAGAAG
AAGCTGTACTGTATCTATGTTGCTATTGGTCAAAAGAGATCCACTGTTGCCCAGTTGGTGAAGAGACTTACAGATGCAGA
TGCCATGAAGTATACCACTGTGGTTTCAGCTACTGCTTCAGATGCTGCCCCACTTCAGTACCTGGCTCCTTATTCTGGAT
GTTCAATGGGAGAATATTTTAGGGATAATGGCAAACACGCTTTGATCATTTATGATGACTTATCCAAACAGGCGGTTGCT
TATCGTCAGATGTCTCTGCTGCTCTGCCGACCCCCTGGTCGTGAGGCCTATCCTGGTGATGTATTCTACCTGCACTCCTG
ACTCCTGGAGAGAGCAGCTAAAATGAGCGATGTTTTTGGTGGTGGCTCCTTGATTGCTCTACCAGTCATCGAAACACAAG
CTGGTAATGTGTCTGCTTACATTCCAACAAATGTCATTTCCATCACTGACAGACAGATCTTCTTGAAAACAGAATTGTTC
TACAAAGGTATCCGCCCTGCCATTAATGTTGGTTTGTCTGTGTCCCATGTCGGATCTGCTGCCCAAACCAGGGCCATGAA
ACAGGTGGCAGGTACTATGAAACTGGAGTTGGCTCAGTATCGTGAGGTTGCTGCTTTTGCCCAGTTCGGTTCTGACCTTG
ATGCTGCCACTCAACAACTCTTGAGTCGTGGTGTGCGTTTGAGTGAGCTGCTCAAGCAGGGACAGTATTCTCCCATGGCT
ATTGAAGAGCAAGTGGCTGTTATCTATGCGGGTGTCAGGGGGTATCTTGACAAGCTGGAGCCCAGCAAGATCACAAAATT
TGAGAATGCTTTCTTGTCTCACGTTATCAGCCAACATCAAGCCCTGTTGGGCAAAATCAGGACTGATGGAAAGATCTCAG
AAGAGTCAGATGCAAAGCTGAAAGAGATTGTAACAAACTTCTTGGCTGGATTTGAAGCT

Alignment

ORF - retro_btau_1426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.02 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNSRLQKTGTAEVSSILEERILGADTSVDLEE
          MLSVRVA.A.A.ALPR..GLVSKNALGSSFIAARNLHASNS.LQKTGTAEVSSILEERILGADTSVDLEE
Retrocopy MLSVRVAVAMACALPRQVGLVSKNALGSSFIAARNLHASNSCLQKTGTAEVSSILEERILGADTSVDLEE

Parental  TGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDV
          TGRVLSIGDGIARVHGLR.VQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDV
Retrocopy TGRVLSIGDGIARVHGLRDVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDV

Parental  PVGEELLGRVVDALGNAIDGKGPIGSKARRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELI
          PVGEELLGRVVDALGNAIDGK.PIGSKARR.VGLKAPGIIPRISV.EPMQTGIKAVDSLVPIGRGQRELI
Retrocopy PVGEELLGRVVDALGNAIDGKSPIGSKARR*VGLKAPGIIPRISVTEPMQTGIKAVDSLVPIGRGQRELI

Parental  IGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATAS
          IGDRQTGK.SIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYT.VVSATAS
Retrocopy IGDRQTGKMSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTTVVSATAS

Parental  DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLE
          DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLL.RPPGREAYPGDVFYLHS.LLE
Retrocopy DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLCRPPGREAYPGDVFYLHS*LLE

Parental  RAAKMNDAFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSA
          RAAKM.D.FGGGSL.ALPVIETQAG.VSAYIPTNVISITD.QIFL.TELFYKGIRPAINVGLSVS.VGSA
Retrocopy RAAKMSDVFGGGSLIALPVIETQAGNVSAYIPTNVISITDRQIFLKTELFYKGIRPAINVGLSVSHVGSA

Parental  AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIYA
          AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRL.ELLKQGQYSPMAIEEQVAVIYA
Retrocopy AQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLSELLKQGQYSPMAIEEQVAVIYA

Parental  GVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA
          GVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA
Retrocopy GVRGYLDKLEPSKITKFENAFLSHVISQHQALLGKIRTDGKISEESDAKLKEIVTNFLAGFEA

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	0.72 RPM	168.20 RPM
ERP005899_muscle	4.17 RPM	989.64 RPM
SRP017611_brain	1.46 RPM	344.01 RPM
SRP017611_kidney	1.84 RPM	820.02 RPM
SRP017611_liver	0.45 RPM	219.35 RPM
SRP030211_testis	0.71 RPM	253.67 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1426 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1426 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,