RetrogeneDB ID: retro_ocun_1445

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:36370348..36371190(-)
• Located in intron of: ENSOCUG00000002928

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSOCUG00000013449
• Aliases: None
• Description: recombination signal binding protein for immunoglobulin kappa J region [Source:HGNC Symbol;Acc:5724]

Sequence

>retro_ocun_1445
AAAAGATTGATAGAGCAAATTGGAAGAGATGGTTGTTCTGAACAAGAGTTTCAACCTTGTGCATTTATTGGAATAGGAAA
TAGTGATCAAGAAATGTAGCAGCCGAACTTGGAAAGAAAGAACTATTGCACAGCCAAAACACTGAAAATATCTGATTCAG
ACAAGAGAAAACACTTCATGTTGTCCATAAATATGTTCTATGGCAACAGTGATGACATTGATGTGTTCCTCAGCAAGCAG
ATAAGAATCATCTCGCAGCCATCCAAAAAGAAACAATCACTGAAAAATGTGGATTTGTGCATTGCCTTAGGTACAAAGGT
GGCTCTATTTAATCGCCTTTGATCCTAGACAATCAGTACCAGATATTTGCTTATAGAAGGAAGTAACTTCCATGCCAGTT
CTCAGCAGTGGGGAGCTTTTTATATTCATCTCCTGGGTGATGATGAATCAGAAGGAGAAGAATTTACAGTCCAAGATGGC
TACATCCATTATGGAAAGACGGTCAAGTTGTGTGTTCAGTTACTGGCATGGCACTCCCAAGATTGATAATTAGGAAAGTT
GATAAGCAGATGGCATCGCTGGATGCAGATGATCCTGTTCTCAACTCCATGAATGTGCATTTACCTTAAGAATAAGGTAA
AATGCACCTTTCTCAAGAAAGAAATAATTTAATTTCAGGTCACTCCATGCTCAAAAGAACCAAATAAAGAAATGATAAAT
GATGGAGCTTCCTGGACAATCGTTAGTACAGACAAGGCAGAGTATAACTTTTATGAGGGAATGGGCCCTGTCCTTGCCCA
GTCACCCCTGTGTGTGTCGTAGTAAGTCTTCAGTTGAATGGC

Alignment

ORF - retro_ocun_1445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.73 %
• Parental protein coverage: 58.81 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KKKKEQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNS
          K...EQ..RDGCSEQE.QPCAFIGIGNSDQEM.Q.NLE.KNYCTAKTL.ISDSDKRKHFMLS..MFYGNS
Retrocopy KRLIEQIGRDGCSEQEFQPCAFIGIGNSDQEM*QPNLERKNYCTAKTLKISDSDKRKHFMLSINMFYGNS

Parental  DDIGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAF
          DDI.VFLSK.I..IS.PSKKKQSLKN.DLCIA.GTKVALFNRL.S.T.STRYL..EG.NFHASSQQWGAF
Retrocopy DDIDVFLSKQIRIISQPSKKKQSLKNVDLCIALGTKVALFNRL*S*TISTRYLLIEGSNFHASSQQWGAF

Parental  YIHLPNVVDDDESEGEEFTVRDGYIHYGQTVKL-VCSVTGMALPRLIIRKVDKQTALLDADDPV-SQLHK
          YIHL.....DDESEGEEFTV.DGYIHYG.TVKL.VCSVTGMALPRLIIRKVDKQ.A.LDADDPV.SQLH.
Retrocopy YIHL---LGDDESEGEEFTVQDGYIHYGKTVKL<VCSVTGMALPRLIIRKVDKQMASLDADDPV<SQLHE

Parental  CAF-YLKDTERMYLCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLA-PVTP
          CAF.YLK.............II.FQ.TPC.KEPNKEMINDGASWTI.STDKAEY.FYEGMGPVLA.PVTP
Retrocopy CAF<YLKN--KVKCTFLKKEII*FQVTPCSKEPNKEMINDGASWTIVSTDKAEYNFYEGMGPVLA<PVTP

Parental  VPVVESLQLNG
          V.VV.SLQLNG
Retrocopy VCVVVSLQLNG

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	38.85 RPM
SRP017611_kidney	0.00 RPM	32.43 RPM
SRP017611_liver	0.08 RPM	15.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1445 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1445 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1445 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445 ,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,