RetrogeneDB ID: retro_ocun_1927

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:52459106..52459989(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_ocun_1927
ATTAAGTCCGGTCCCGCCATTCAAGCTGGCATTGACCTTACAGCGGGGGCTGCAGGGGCACAGCCTGCGTGCTGACAGGG
CAGCCCTTTGACACGATGAAAGTGAAGATGCAGGCGTTCCGTGACCTGTACCAGGGCCTCAACGACTGCTGCCTGAAGAC
CTACACCGGGTGGGCGTCTACGGCTTCTACAAGGGGAGCAGCCCGGCGCTGATCGCCCACATCGCCGAGAACTTGGTGCT
CTTCATGTGCTACGACTTCTACCAGCAGGTCGTGCAGAAAGTGCTGGGACTGGACTAGCAGGCAAAGCTCAGCGACCTGC
AGAACGCTGCAGCTGGCTCCTTCGCTTCCGCCTTCACCGTGCTGGTGCTTGGCCCCACGGAGCTGGTGAAGTGCCGCCTC
CAAGCCATGCAGGAGATGGAGACTTCGGGAAAGATCGCCAATAGCCAGAACAGAATTTGGTCTGTCGTGAAGAGCATCCT
TACAAAGCATGGCCCCTTAGGCTTCTACCACAGACTGTCAAGCACTTTACTTCGGGAAGTACCGGGCTATGTCTTCGGTG
GTTATGAACTGAACTGATCCTTCTTTGCATCAGGGAGATCAAAAGACGAACTAGGTCCTGTCCCTTTGATGTTAAGTGGC
GGAGTTGGTGGGATTTGCCTCTGGCTTGCTGTATACCCTGTGGACTGCATCAAATCCAAAATTCAAGTTCTTTCCATGAC
TGGCAAATAAGGGGGATTTATGGGGACTTTTCTAAGTGTTGTGAGGCACGAAGGAATAGCAACCTTATATTCTGGACTGA
AACCTACTATGATTGGAGCATTCCCTGCCAATGGGGCACTATTTTTGGCCTAGGAGAACAGCACGAAATTGATGATGAGC
CAG

Alignment

ORF - retro_ocun_1927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.95 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKSNPAIQAAIDLTAGAAG-GTACVLTGQPFDTMKVKMQTFPDLYRGLSDCCLKTYA-QVGVRGFYKGTS
          .KS.PAIQA.IDLTAGAAG.GTACVLTGQPFDTMKVKMQ.F.DLY.GL.DCCLKTY...VGV.GFYKG.S
Retrocopy IKSGPAIQAGIDLTAGAAG<GTACVLTGQPFDTMKVKMQAFRDLYQGLNDCCLKTYT<RVGVYGFYKGSS

Parental  PALIANIAENSVLFMCYGFCQQVVRKVGGLDKQAKLSDLQNAAAGSFASAFAALVLCPTELVKCRLQAMH
          PALIA.IAEN.VLFMCY.F.QQVV.KV.GLD.QAKLSDLQNAAAGSFASAF..LVL.PTELVKCRLQAM.
Retrocopy PALIAHIAENLVLFMCYDFYQQVVQKVLGLD*QAKLSDLQNAAAGSFASAFTVLVLGPTELVKCRLQAMQ

Parental  EMETSGKIVNSQNTVWSVVKSILRKDGPLGFYHGLSSTLLREVPGYFFFFGGYELSRSFFASGRSKDELG
          EMETSGKI.NSQN..WSVVKSIL.K.GPLGFYH.LSSTLLREVPGY...FGGYEL..SFFASGRSKDELG
Retrocopy EMETSGKIANSQNRIWSVVKSILTKHGPLGFYHRLSSTLLREVPGY--VFGGYELN*SFFASGRSKDELG

Parental  PVPLMLSGGVGGICLWLAVYPVDCIKSRIQVMSMSGKQAGFTGTLLSVVRNEGIAALYSGLKPTMIRAFP
          PVPLMLSGGVGGICLWLAVYPVDCIKS.IQV.SM.GK..GF.GT.LSVVR.EGIA.LYSGLKPTMI.AFP
Retrocopy PVPLMLSGGVGGICLWLAVYPVDCIKSKIQVLSMTGK*GGFMGTFLSVVRHEGIATLYSGLKPTMIGAFP

Parental  ANGALFLAYEYSRKLMMSQ
          ANGALFLA.E.S.KLMMSQ
Retrocopy ANGALFLA*ENSTKLMMSQ

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	0.06 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_1927 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1927 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
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,