RetrogeneDB ID: retro_ocun_617

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:80006802..80007352(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000027616
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017097
• Aliases: None
• Description: None

Sequence

>retro_ocun_617
TTGGCAGTGGTGGTGGCAGTGGCGACATCTGGTGTCCTGGGGCTGGAGGACTCAGTGCTGTTCCGGTGCAGAATGGGCCG
GAGTGCTGATTCTGACATTTGGGATGATACAGCATTGGTAAAAGCTTATGGTAAAGCTATAGCATCATTTACGCATGCAC
TGAAGAATGGTGGCATTTGTGAAGCTTCAGATCAACCAAAGGTCATAACTAAAAGAAAATCTGTTAAGAAGAATAAATGC
CAAACGAGGAATACTGCAACTGCCTTGAAACAGTGGAAGGTTGGTAAAAAATGTTCTGCCATTTGGTCTGAAGATGGCTG
CATCTCCCCAGCTACAATTGATTCAGTTGATCTTAAGAGGGAAACCTGTGTTGTGGTTTACACTGGATATGGATATAGAG
AAGAGCAAAATCTGTCTGTTCTACTTTTCCCAGACATCTGAAGTAGCTAATAACACAGAACAAAATGCTCAGTAGAATGA
AAATGAGAGTCAAGTTTCCAGTGAGGACTTCTCCAGGACTCCTGGAAATAAATAATATCAAGTCAAAAGC

Alignment

ORF - retro_ocun_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.05 %
• Parental protein coverage: 65.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTMAMGSGGGGVSEPEDSVLFRRGTGQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICATSDKPKVTP
          L.........GV...EDSVLFR...G.S.DSDIWDDTAL.KAY.KA.ASF.HALKNG.IC..SD.PKV..
Retrocopy LAVVVAVATSGVLGLEDSVLFRCRMGRSADSDIWDDTALVKAYGKAIASFTHALKNGGICEASDQPKVIT

Parental  KRKPVKKNKCQKKKTTTALKQWKVGDKCCAIWSEDGCVYPATIASVDFKRETCVVVYTGYGNREEQNLSD
          KRK.VKKNKCQ...T.TALKQWKVG.KC.AIWSEDGC..PATI.SVD.KRETCVVVYTGYG.REEQNLS.
Retrocopy KRKSVKKNKCQTRNTATALKQWKVGKKCSAIWSEDGCISPATIDSVDLKRETCVVVYTGYGYREEQNLSV

Parental  LLSP-TSEVANNIEHNAQENENESQVSTDESENSSRSPGSKPNNIKS
          LL.P.TSEVANN.E.NAQ.NENESQVS...SE..SR.PG.K....KS
Retrocopy LLFP>TSEVANNTEQNAQ*NENESQVS---SEDFSRTPGNK*YQVKS

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	6.13 RPM
SRP017611_kidney	0.00 RPM	10.34 RPM
SRP017611_liver	0.00 RPM	2.08 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_617 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_617 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_617 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012328	1 retrocopy	retro_cpor_988,
Dasypus novemcinctus	ENSDNOG00000007283	4 retrocopies	retro_dnov_1239, retro_dnov_1613, retro_dnov_1637, retro_dnov_2175,
Echinops telfairi	ENSETEG00000001406	2 retrocopies	retro_etel_1549, retro_etel_2012,
Homo sapiens	ENSG00000205571	1 retrocopy	retro_hsap_4140,
Gorilla gorilla	ENSGGOG00000026704	1 retrocopy	retro_ggor_2780,
Myotis lucifugus	ENSMLUG00000010603	1 retrocopy	retro_mluc_1623,
Macaca mulatta	ENSMMUG00000020214	1 retrocopy	retro_mmul_216,
Nomascus leucogenys	ENSNLEG00000004454	1 retrocopy	retro_nleu_1054,
Oryctolagus cuniculus	ENSOCUG00000017097	1 retrocopy	retro_ocun_617 ,
Pan troglodytes	ENSPTRG00000016955	1 retrocopy	retro_ptro_2813,
Sus scrofa	ENSSSCG00000016970	1 retrocopy	retro_sscr_654,
Ictidomys tridecemlineatus	ENSSTOG00000012288	1 retrocopy	retro_itri_968,
Tupaia belangeri	ENSTBEG00000002399	1 retrocopy	retro_tbel_1033,