RetrogeneDB ID: retro_ocun_1762

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018862:328865..329437(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YBX2
• Ensembl ID: ENSOCUG00000015064
• Aliases: None
• Description: Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]

Sequence

>retro_ocun_1762
CCGGTGAAGGGCAGCCGCTACGCCCCCAATCGACGCAGGTTCCGCCACTTCATCCCCCGGCCTCGCCCAGCTGCCCCGCT
GCCCATGGTGGCAGAGGTGCCCCCGGCGGGACAGAACCCGGCAGTGTAGGAGAGCGGGCTGAAGACTGGGCAGTGGCTCA
GGCGACAGCGCCCACCACCCTTTTTCTACCGACTGCGGGTTGTGCGAGGCCCTCGTCCCCCAACCAGTAGCAGCCCATAG
AGGGCACTGATGGGGTGGAGCCCAAAGACACAGCCCTGTTGGAGGGGGACCAACAGCAGGGTGATGAGCGGGTGCCCCCA
CCCAGTTTCCGGCCCAGATATCACAGGCCCTTCCGCCTGAGGCCACCCCAGCAGCCTAGCACAGAAGGTGGGGATGGGGA
GACCAAGCCCAGCCAAGGCCCCACTGATGGCTCCTGGCCTGAACCCCAGCACCCACGAAACCGCCCCTACTTCCAGCTGC
GATGGCAGCAGCCCCCTGGCCCTCAGCAGCCCACTGCCCCAGAGACCTCAGCCCCCATCAACAGTGGGGATCCCCCCCCC
ACCATGCTGGAG

Alignment

ORF - retro_ocun_1762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.38 %
• Parental protein coverage: 61.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVKGSRYAPNRRRFRRFIPRPRPAAPPPMVAEVPSGGTEPGSEGERAEDSGQRPRRRRPPPFFYRRRFVR
          PVKGSRYAPNRRRFR.FIPRPRPAAP.PMVAEVP..G..P....E.....GQ..RR.RPPPFFYR.R.VR
Retrocopy PVKGSRYAPNRRRFRHFIPRPRPAAPLPMVAEVPPAGQNP-AV*ESGLKTGQWLRRQRPPPFFYRLRVVR

Parental  GPRPP-NQQQPIEGTNGVEPKDTAPLEGDQQQGDERVPPPRFRPRYRRPFRPRPPQQPTTEGGDGETKPS
          GPRPP.NQ.QPIEGT.GVEPKDTA.LEGDQQQGDERVPPP.FRPRY.RPFR.RPPQQP.TEGGDGETKPS
Retrocopy GPRPP<NQ*QPIEGTDGVEPKDTALLEGDQQQGDERVPPPSFRPRYHRPFRLRPPQQPSTEGGDGETKPS

Parental  QGPTDGSRPEPQRPRNRPYFQRRRQQPPGPRQPSAPETSAPINSGDPPPTMLE
          QGPTDGS.PEPQ.PRNRPYFQ.R.QQPPGP.QP.APETSAPINSGDPPPTMLE
Retrocopy QGPTDGSWPEPQHPRNRPYFQLRWQQPPGPQQPTAPETSAPINSGDPPPTMLE

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	0.17 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1762 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1762 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1762 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016581	1 retrocopy	retro_cjac_1473,
Homo sapiens	ENSG00000006047	1 retrocopy	retro_hsap_637,
Macaca mulatta	ENSMMUG00000022712	1 retrocopy	retro_mmul_2237,
Nomascus leucogenys	ENSNLEG00000008063	1 retrocopy	retro_nleu_1954,
Oryctolagus cuniculus	ENSOCUG00000015064	1 retrocopy	retro_ocun_1762 ,
Oryctolagus cuniculus	ENSOCUG00000028047	2 retrocopies	retro_ocun_1519, retro_ocun_1953,
Pan troglodytes	ENSPTRG00000008673	3 retrocopies	retro_ptro_1264, retro_ptro_464, retro_ptro_50,