RetrogeneDB ID: retro_ocun_1570

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:9284277..9284822(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR61
• Ensembl ID: ENSOCUG00000009040
• Aliases: None
• Description: WD repeat domain 61 [Source:HGNC Symbol;Acc:30300]

Sequence

>retro_ocun_1570
ATTGCCCTAAAGGGGAATGTAGGGAAAGTGAACATTTCTGGTATGGAAAGTAGGAAAAAAGAGTATTTCTTGGACACAAG
AGGGAAATTCATTCTCAGTATTGCATATAGTCTCTACGGGAAGCACCTGGCCAATAGAGCCATAGATGGCAACATCAGTA
TTTTTGACATCACAACTGGGAAGCATCTGCATACTCTGGAAGGCCATGCCATGCCCATTCACTCCTTAACCTTTTCCCGG
ATTTGCGCCTCCTCGTCACTGCCTCAGATTATGGCTATCTCAAGATCTGTGATGCACAGCACGCCAGCCTGGCTGGCACA
CTTAGTGGACATGCCTCCTGGGTGCTGTCACCCTTTGTCCTGACGACACACACTTTGTTTCTAGTTCATCTGACAAAGTG
TAAATGTCTGGGATGTTGGGACGAGGACCTGTATCCACAACTTTTTTGATCCGTAGGATCAGGTCTGGGAGTAAAATGCA
GTGGAAAGGCCTCAAAAGTTGTGTCTGTTGGTAATGACCAGGAAATCCACATGTACAGCTGTCCA

Alignment

ORF - retro_ocun_1570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.89 %
• Parental protein coverage: 59.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LATGTHVGKVNIFGVESGKKEYSLDTRGKFILSIAYSPDGKYLASGAIDGIINIFDIATGKLLHTLEGHA
          .A....VGKVNI.G.ES.KKEY.LDTRGKFILSIAYS..GK.LA..AIDG.I.IFDI.TGK.LHTLEGHA
Retrocopy IALKGNVGKVNISGMESRKKEYFLDTRGKFILSIAYSLYGKHLANRAIDGNISIFDITTGKHLHTLEGHA

Parental  MPIRSLTFS-PDSQLLVTASDDGYIKIYDV---STCSSLCKVCAWI-DAVVSYCRSLF-DSSSDK-SVKV
          MPI.SLTFS.PD..LLVTASD.GY.KI.D....S....L.....W.....V.....LF..SSSDK.SV.V
Retrocopy MPIHSLTFS<PDLRLLVTASDYGYLKICDAQHASLAGTLSGHASWVLSPFVLTTHTLF<SSSSDK<SVNV

Parental  WDVGTRTCVHTFFDHQDQVW-GVKYNGQRLEFVDTGRIFPLYWECCP
          WDVGTRTC.H.FFD..DQVW.GVK..G.....V..G.........CP
Retrocopy WDVGTRTCIHNFFDP*DQVW<GVKCSGKASKVVSVGNDQEIHMYSCP

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	34.99 RPM
SRP017611_kidney	0.00 RPM	26.66 RPM
SRP017611_liver	0.00 RPM	8.71 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1570 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1570 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015944	1 retrocopy	retro_btau_702,
Canis familiaris	ENSCAFG00000014230	3 retrocopies	retro_cfam_1378, retro_cfam_1422, retro_cfam_910,
Echinops telfairi	ENSETEG00000004321	1 retrocopy	retro_etel_1046,
Macropus eugenii	ENSMEUG00000015991	1 retrocopy	retro_meug_744,
Oryctolagus cuniculus	ENSOCUG00000009040	1 retrocopy	retro_ocun_1570 ,
Ictidomys tridecemlineatus	ENSSTOG00000007784	1 retrocopy	retro_itri_843,
Tupaia belangeri	ENSTBEG00000009390	1 retrocopy	retro_tbel_48,