RetrogeneDB ID: retro_ocun_192

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:23332449..23333355(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000001192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000016684
• Aliases: None
• Description: None

Sequence

>retro_ocun_192
ATGAAGAACAGCCCCGGCCTCCAGGCCGCCATCGACCTCACGGCGGGTGCGGTGGGGGGCACGGCGTGCGTACTCACCGG
GCAGCCCTTCGACACGATGAAAGTCAAGATGCAGGCGTTCCCCAGCCTGTACTCGGGCCTCACCGACTGCTTCCTGAAGA
CCTACTCCCACGTGGGGTTGCGGGGCCTCTACAGGGGCACAGGCCCCGCACTGATGGCCTATGTGGCCCAGAACTCTGTC
CTCTTCATGTGCTACGGTTTCTGCCAGAAGTTTGTCAGGAGCGTGGCCGGACTGGACAAGAAGGCGAAGCTGAACGACCT
GCAGTCTGCGGCCGCGGGCTCCCTGGCCTCGGCGTTCGCCGCGCTGGCCCTCTGCCCCACTGAGCTGGTCAAGTGCCGGC
TGCAGACCATGTACGAGTTGCAGCTATTAGGGAAGATAGCAAAGAGCCATAATACAATTTGGTCTGTGGTGAAGAGCATC
CTCAGAAAGGACGGCCCCTTAGGCTTCTACTACGGACTCTCGAGCACTCTGCTGCAAGAAGTACCGGGCTATTTCTTCTT
CTTCGGGGGCTACGAACTGAGCCGATCGTTTTTTGCCTCAGGCAGATCAAAAGATGAACTAGGTCCAGTTCCATTGATGT
TAAGCGGTGGAGTTGCTGGAATCTGCCTCTGGCTTGTCATATTCCCAGTGGATTGTATTAAGTCCAGAATTCAAGTTCTT
TCCATGTATGGAAAACAGGCAGGATTTTTTGGAACTCTTTTGGGCATTGTGAAATATGAAGGAATAGCAGCCTTATACTC
TGGACTGAAACCTACCATGGTTCGAGCAGTCCCTGCCAATGGGGCACTATTTTTGGCCTATGAGTACAGTAGGAAGATGA
TGATGAGCCAGTTGGAACCCTGCTGA

Alignment

ORF - retro_ocun_192 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.27 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAGGTACVLTGQPFDTMKVKMQTFPDLYRGLSDCCLKTYAQVGVRGFYKGTSPA
          MK..P..QAAIDLTAGA.GGTACVLTGQPFDTMKVKMQ.FP.LY.GL.DC.LKTY..VG.RG.Y.GT.PA
Retrocopy MKNSPGLQAAIDLTAGAVGGTACVLTGQPFDTMKVKMQAFPSLYSGLTDCFLKTYSHVGLRGLYRGTGPA

Parental  LIANIAENSVLFMCYGFCQQVVRKVGGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQAMHEM
          L.A..A.NSVLFMCYGFCQ..VR.V.GLDK.AKL.DLQ.AAAGS.ASAFAAL.LCPTELVKCRLQ.M.E.
Retrocopy LMAYVAQNSVLFMCYGFCQKFVRSVAGLDKKAKLNDLQSAAAGSLASAFAALALCPTELVKCRLQTMYEL

Parental  ETSGKIVNSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELGPV
          ...GKI..S.NT.WSVVKSILRKDGPLGFY.GLSSTLL.EVPGYFFFFGGYELSRSFFASGRSKDELGPV
Retrocopy QLLGKIAKSHNTIWSVVKSILRKDGPLGFYYGLSSTLLQEVPGYFFFFGGYELSRSFFASGRSKDELGPV

Parental  PLMLSGGVGGICLWLAVYPVDCIKSRIQVMSMSGKQAGFTGTLLSVVRNEGIAALYSGLKPTMIRAFPAN
          PLMLSGGV.GICLWL...PVDCIKSRIQV.SM.GKQAGF.GTLL..V..EGIAALYSGLKPTM.RA.PAN
Retrocopy PLMLSGGVAGICLWLVIFPVDCIKSRIQVLSMYGKQAGFFGTLLGIVKYEGIAALYSGLKPTMVRAVPAN

Parental  GALFLAYEYSRKLMMSQFE
          GALFLAYEYSRK.MMSQ.E
Retrocopy GALFLAYEYSRKMMMSQLE

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	0.00 RPM	6.62 RPM
SRP017611_kidney	0.00 RPM	9.32 RPM
SRP017611_liver	0.00 RPM	87.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_192 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_192 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_192 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_72

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011723	1 retrocopy	retro_amel_5,
Bos taurus	ENSBTAG00000011647	1 retrocopy	retro_btau_1581,
Canis familiaris	ENSCAFG00000005955	1 retrocopy	retro_cfam_211,
Choloepus hoffmanni	ENSCHOG00000004899	3 retrocopies	retro_chof_1643, retro_chof_494, retro_chof_561,
Erinaceus europaeus	ENSEEUG00000014870	1 retrocopy	retro_eeur_329,
Mus musculus	ENSMUSG00000031482	1 retrocopy	retro_mmus_75,
Oryctolagus cuniculus	ENSOCUG00000016684	2 retrocopies	retro_ocun_192 , retro_ocun_1927,
Ochotona princeps	ENSOPRG00000014616	1 retrocopy	retro_opri_7,
Rattus norvegicus	ENSRNOG00000011881	1 retrocopy	retro_rnor_130,
Sorex araneus	ENSSARG00000002472	1 retrocopy	retro_sara_30,
Sus scrofa	ENSSSCG00000009373	1 retrocopy	retro_sscr_688,