RetrogeneDB ID: retro_ocun_1861

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019507:2158..3182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2A
• Ensembl ID: ENSOCUG00000016095
• Aliases: None
• Description: eukaryotic translation initiation factor 2A, 65kDa [Source:HGNC Symbol;Acc:3254]

Sequence

>retro_ocun_1861
GCCATACATGTTCCAGGAAGCAAAGGTGCACCTTCGTATGTTAGATTGTATCAGTACCCCAACTTTGGTGGACCTCATGC
AGCTTTAGCCAATAAAAGTTTCTTTAAGGCTGATAAGTTTACAATGCTATGGAATAAAAAAGCTACTGCTGTCTCGGTAA
TAGCTAGTACAAACGATGATAAGACAGGAGCTTCCTATTATGGGGAACAGAGTTGCATTACATTGCAACAAATAGAGAGA
GTGCCATAGCACAACTACCAAAAGGTGGCCCTATTTATGACGTTTGGAATTCTAGTTCTACTGAATTTTGTGCTGTATAT
GGTTTTAAAGCCTACCAAAACAACACTTTTCAACTTGAAATGTGATCCTGTGTTTGACTTTGGAACTGGTCCTCAGAATG
CAGGCTACTATAGCCCTCAAGGACATATATTAGTACTAGCTGGATTTGGAAATCTGAGAGGACAAATGGAAGTGTGGGAT
GTTAAAAACTACAAGCTATTTCTAAACCAGTGGCTTCTGATTCTACATATTTTGCTTGGTGCCCAGATGGTGAGCATATT
TTAACAGCCACATGTGCTCCCAGGTTACGTGTTAATAATGGGTATGAGATTTGGCATTATACTGGCTCTATATTGCACAA
ATATGATGTGCCCTCAAGTGGAGACCTATGGCAGGTTTCATGGCAGCCACTTTTGGATGGAATATTTCCAACAAAACCAA
TAACTTACCAAGCAGTTCCAAGTGAAGTACCCAGTGAGGAAATAAAGTTGCAACAGCCTATAGATGCCCTGCTTTCAGAA
ATAAGCTAGTCACTAATTCCAAGCTGCATGAAGAGGAGCCACCTCAGAATATGAAACCACAATCAGGAAATGATAAACCC
TCATCAAAAACAGCCCTTAAAAAATCAAAGGAAACACAAAGCAGTTAAGAAAGCTGTAAAGCAGGAAGCAAGAAGTGACA
AATGTCCAGATTTGCCCTCTACTCCTGTGCCACAAAGCACCCACAAACCATTACCTCTCAGTCA

Alignment

ORF - retro_ocun_1861 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.39 %
• Parental protein coverage: 58.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  AVYVPGSKGAPSFVRLYQYPNFGGPHAALANKSFFKADKVTMLWNKKATAVLVIASTDVDKTGASYYGEQ
          A..VPGSKGAPS.VRLYQYPNFGGPHAALANKSFFKADK.TMLWNKKATAV.VIAST..DKTGASYYGEQ
Retrocopy AIHVPGSKGAPSYVRLYQYPNFGGPHAALANKSFFKADKFTMLWNKKATAVSVIASTNDDKTGASYYGEQ

Parental  T-LHYIATNGESAVVQLPKGGPIYDVAWNSSSTEFCAVYGFM-PAKATIFNLKCDPVFDFGTGPRNAAYY
          ..LHYIATN.ESA..QLPKGGPIYDV.WNSSSTEFCAVYGF..P.K.T.FNLKCDPVFDFGTGP.NA.YY
Retrocopy S<LHYIATNRESAIAQLPKGGPIYDV-WNSSSTEFCAVYGFK>PTKTTLFNLKCDPVFDFGTGPQNAGYY

Parental  SPQGHILVLAGFGNLRGQMEVWDVKNYKL-ISKPVASDSTYFAWCPDGEHILTATCAPRLRVNNGYKIWH
          SPQGHILVLAGFGNLRGQMEVWDVKNYKL.ISKPVASDSTYFAWCPDGEHILTATCAPRLRVNNGY.IWH
Retrocopy SPQGHILVLAGFGNLRGQMEVWDVKNYKL<ISKPVASDSTYFAWCPDGEHILTATCAPRLRVNNGYEIWH

Parental  YTGSVLHKYDVPSNGELWQVSWQPFLDGIFPAKAITYQAVPSEVPSEE-PKVATAYRPPALRNKPVTNSK
          YTGS.LHKYDVPS.G.LWQVSWQP.LDGIFP.K.ITYQAVPSEVPSEE..KVATAYR.PA.RNK.VTNSK
Retrocopy YTGSILHKYDVPSSGDLWQVSWQPLLDGIFPTKPITYQAVPSEVPSEE<NKVATAYRCPAFRNKLVTNSK

Parental  LHEEEPPQNMKPQSGSDKPLSKTA-LKNQRKHEA-KKAAKQEARSDKSPDLPSTPAPQST-PRNITSQS
          LHEEEPPQNMKPQSG.DKP.SKTA.LKNQRKH.A.KKA.KQEARSDK.PDLPSTP.PQST.P..ITSQS
Retrocopy LHEEEPPQNMKPQSGNDKPSSKTA>LKNQRKHKAVKKAVKQEARSDKCPDLPSTPVPQST<PQTITSQS

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	39.24 RPM
SRP017611_kidney	0.00 RPM	42.47 RPM
SRP017611_liver	0.00 RPM	16.42 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1861 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1861 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1861 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001199	1 retrocopy	retro_cjac_968,
Dasypus novemcinctus	ENSDNOG00000014002	1 retrocopy	retro_dnov_1148,
Homo sapiens	ENSG00000144895	1 retrocopy	retro_hsap_565,
Gorilla gorilla	ENSGGOG00000015391	1 retrocopy	retro_ggor_509,
Loxodonta africana	ENSLAFG00000003767	1 retrocopy	retro_lafr_502,
Macaca mulatta	ENSMMUG00000017696	1 retrocopy	retro_mmul_2395,
Monodelphis domestica	ENSMODG00000028858	1 retrocopy	retro_mdom_618,
Nomascus leucogenys	ENSNLEG00000003219	1 retrocopy	retro_nleu_2213,
Oryctolagus cuniculus	ENSOCUG00000016095	3 retrocopies	retro_ocun_1771, retro_ocun_1825, retro_ocun_1861 ,
Pongo abelii	ENSPPYG00000029636	2 retrocopies	retro_pabe_517, retro_pabe_652,
Pan troglodytes	ENSPTRG00000015528	1 retrocopy	retro_ptro_423,
Ictidomys tridecemlineatus	ENSSTOG00000003374	1 retrocopy	retro_itri_1706,