RetrogeneDB ID: retro_ocun_1235

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:66953117..66954771(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSOCUG00000003967
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]

Sequence

>retro_ocun_1235
ATGCTGTCCGTGCGTGTAGCCGCGGCCGTGGCCCGCGCCCTTCCCCGGCGGGCCGGACTGGTCTCCAAAAATGCTTTGGG
ATCATCTTTTATTGCAGCAAGGAACCTTCATGCCTCTAACACGCGTCTTCAGAAGACTGGCACTGCTGAGATGTCCTCTA
TTCTTGAAGAGCGAATTCTTGGAGCTGATACCTCTGTTGACCTTGAAGAGACTGGGAGTGTCTTAAGTATTGGTGATGGT
ATTGCCCGAATACACGGGCTCCAGAATGTTCAAGCAGAAGAAATGGTAGAGTTTTCCTCAGGCTTAAAGGGTATGTCTCT
GAACTTGGAGCCCGACAATGTTGGTGTTGTGTTTGGGAATGATAAACTCATCAAGGAAGGAGATATTGTGAAGAGGACAG
GTGCCATTGTGGATGTTCCAGTTGGTGAGGAGCTGTTGGGTCGTGTAGTAGATGCCCTTGGTAATGCCATTGATGGAAAG
GGTCCAATTGGTTCCAAGACTCGTAGGCGAGTTGGCCTGAAAGCCCCTGGAATCATTCCTCGAATCTCGGTGCGGGAACC
AATGCAAACTGGCATTAAGGCTGTGGATAGCTTGGTGCCGATTGGTCGTGGTCAGCGTGAGCTGATTATTGGTGACAGAC
AGACAGGGAAAACATCCACTGCTATTGACACAATTATTAATCAGAAACGTTTCAATGATGGAACTGATGAAAAGAAGAAG
CTGTACTGCATCTATGTTGCTATTGGTCAGAAGAGATCCACTGTTGCCCAGTTGGTGAAGAGACTGACAGATGCAAATGC
CATGAAGCACACCATTGTGGTGTCAGCTACTGCTTCGGATGCTGCCCCACTTCAGTACCTGGCTCCTTATTCTGGCTGTT
CTATGGGAGAGTACTTTAGAGATAACGGCAAGCACGCTTTGATCATCTATGACGACTTGTCCAAACAGGCTGTTGCTTAC
CGCCAGATGTCGCTGTTGCTCCGCCGGCCCCCTGGTCGTGAGGGCCTACCCTGGTGATGTGTTCTACCTACACTCCCGGC
TGCTGGAGAGAGCAGCCAAAATGAACGACTCTTTTGGTGGTGGCTCCTTGACTGCGTTACCAGTCATAGAAACACAGGCT
GGGGATGTGTCTGCTTACATTCCAACCAATGTCATTTCCATCACTGATGGACAGATCTTGGAAACAGAATTGTTCTATAA
AGGTATCCGCCCTGCCATTAATGTGGGTTTGTCTGTGTCCCGTGTCGGATCTGCTGCCCAAACCAGAGCTATGAAGCAGG
TGGCAGGTACCATGAAGCTGGAATTGGCGCAGTATCGTGAGGTTGCTGCTTTTGCTCAGTTTGGTTCTGACCTTGATGCT
GCCACTCAACAACTCTTGAGTCGTGGTGTGCGTCTGACGGAGTTGCTGAAGCAAGGACAGTATTCTCCCATGGCTATTGA
AGAACAAGTGGCTGTTATCTATGCGGGTGTGAGGGGGTACCTTGATAAATTGGAGCCCAGCAAGATCACAAAATTTGAGA
ATGCTTTCTTGTCGCATGTTGTCAGCCAACATCAAGCCCTGTTGGGTAATATCAGGACTGAAGGGAAGATCTCAGAAGAG
TCGGATGCCAAGCTGAAGGAGATTGTAACAAACTTCTTGGCTGGATTTGAAGCT

Alignment

ORF - retro_ocun_1235 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNTRLQKTGTAEMSSILEERILGADTSVDLEE
          MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNTRLQKTGTAEMSSILEERILGADTSVDLEE
Retrocopy MLSVRVAAAVARALPRRAGLVSKNALGSSFIAARNLHASNTRLQKTGTAEMSSILEERILGADTSVDLEE

Parental  TGRVLSIGDGIARVHGLRNVQAEEMVEFSSGLKGMSLNLEPDNVGVVVFGNDKLIKEGDIVKRTGAIVDV
          TG.VLSIGDGIAR.HGL.NVQAEEMVEFSSGLKGMSLNLEPDNVG.VVFGNDKLIKEGDIVKRTGAIVDV
Retrocopy TGSVLSIGDGIARIHGLQNVQAEEMVEFSSGLKGMSLNLEPDNVG-VVFGNDKLIKEGDIVKRTGAIVDV

Parental  PVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELI
          PVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELI
Retrocopy PVGEELLGRVVDALGNAIDGKGPIGSKTRRRVGLKAPGIIPRISVREPMQTGIKAVDSLVPIGRGQRELI

Parental  IGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMKYTIVVSATAS
          IGDRQTGKTS.AIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDA.AMK.TIVVSATAS
Retrocopy IGDRQTGKTSTAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDANAMKHTIVVSATAS

Parental  DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGRE-AYPGDVFYLHSRLL
          DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGRE.AYPGDVFYLHSRLL
Retrocopy DAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGRE>AYPGDVFYLHSRLL

Parental  ERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGS
          ERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQI.LETELFYKGIRPAINVGLSVSRVGS
Retrocopy ERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQI-LETELFYKGIRPAINVGLSVSRVGS

Parental  AAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIY
          AAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIY
Retrocopy AAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQYSPMAIEEQVAVIY

Parental  AGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGNIRTDGKISEESDAKLKEIVTNFLAGFEA
          AGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGNIRT.GKISEESDAKLKEIVTNFLAGFEA
Retrocopy AGVRGYLDKLEPSKITKFENAFLSHVVSQHQALLGNIRTEGKISEESDAKLKEIVTNFLAGFEA

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
SRP017611_brain	15.45 RPM	605.42 RPM
SRP017611_kidney	7.50 RPM	1031.00 RPM
SRP017611_liver	5.55 RPM	267.60 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1235 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1235 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1235 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 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,
Macropus eugenii	ENSMEUG00000009770	1 retrocopy	retro_meug_151,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235 ,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,