RetrogeneDB ID: retro_ocun_1194

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:71943734..71944306(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COPS7B
• Ensembl ID: ENSOCUG00000016918
• Aliases: None
• Description: COP9 signalosome subunit 7B [Source:HGNC Symbol;Acc:16760]

Sequence

>retro_ocun_1194
GGCAAACAAGGAGATTACATAGCCAACAAGGAGAGCCTGCCAGAACTGAGCACAGCCCAGCAGAACAAGCTGAAATATCT
GACCATCATGAGCCTGACATTGAGAATAAAGTGCATTCCCTACACTGTGCTGCTGAAAGACCTGTGGATGCAGAATCTCC
AGGAACTGGAAGACCTCATCATTGAGGCTGTCTACACTGACATCACCCAGGGCAAGCTGGACCAGTAAAACCAACTGCCA
CAAGTGGACTTCTGCATTGGCCATGACATCCGAAAGAAGGTTAGCAATAACACTGTTAAGACCTTGCATGAATAGTGTGA
TGGCTGTGAAGCGGTTCTGCTTGGCATTGAGCATCAGGTCCTGAGAGCCAGCCAGTACAAAGAGAACCACAACCGGGCTC
AGCAGCAGGTGGAAGAAGAGGTTACCAACATCAAGAAGACGCTCAAAGCCACCACGTCCTTCTCGGCCCTGGAAATGGAG
CAGCAGCTGGCCAAGAGGGAGTGTTTCCCTCATGCTGAGCAGAAGCAGCCCACCAAGATGTCCAAAGTGAAAGTCTCATC
TTCAGCCACCAC

Alignment

ORF - retro_ocun_1194 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.83 %
• Parental protein coverage: 72.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMRNLRELEDLIIEAVYTDIIQ
          G...DYIANKESLPELSTAQQNKLK.LTI.SL..R.KCIPY.VLLKDL.M.NL.ELEDLIIEAVYTDI.Q
Retrocopy GKQGDYIANKESLPELSTAQQNKLKYLTIMSLTLRIKCIPYTVLLKDLWMQNLQELEDLIIEAVYTDITQ

Parental  GKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCEAVLLGIEQQVLRANQYKENHNRTQQQVEAE
          GKLDQ.NQL..VDFCIG.DIRKK..NN.VKTLHE.CDGCEAVLLGIE.QVLRA.QYKENHNR.QQQVE.E
Retrocopy GKLDQ*NQLPQVDFCIGHDIRKKVSNNTVKTLHE*CDGCEAVLLGIEHQVLRASQYKENHNRAQQQVEEE

Parental  VTNIKKTLKATASSSAQEMEQQLAERECPPHAEQRQPTKKMSKVK-GLVSSRH
          VTNIKKTLKAT.S.SA.EMEQQLA.REC.PHAEQ.QPT.KMSKVK..L..S.H
Retrocopy VTNIKKTLKATTSFSALEMEQQLAKRECFPHAEQKQPT-KMSKVK<SLIFSHH

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	23.68 RPM
SRP017611_kidney	0.30 RPM	11.55 RPM
SRP017611_liver	0.00 RPM	4.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1194 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1194 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1194 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013630	1 retrocopy	retro_cjac_3894,
Oryctolagus cuniculus	ENSOCUG00000011187	1 retrocopy	retro_ocun_1086,
Oryctolagus cuniculus	ENSOCUG00000016918	1 retrocopy	retro_ocun_1194 ,
Ochotona princeps	ENSOPRG00000008376	1 retrocopy	retro_opri_850,
Sarcophilus harrisii	ENSSHAG00000009961	1 retrocopy	retro_shar_537,