RetrogeneDB ID: retro_ocun_1766

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018874:163816..164314(-)
• Located in intron of: ENSOCUG00000012642

Retrocopy information

• Ensembl ID: ENSOCUG00000025502
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GYG1
• Ensembl ID: ENSOCUG00000003516
• Aliases: GYG1, GYG
• Description: glycogenin 1 (GYG1), mRNA [Source:RefSeq mRNA;Acc:NM_001082241]

Sequence

>retro_ocun_1766
ATGACAGATCAGGCCTTTGTGACACTGACCACAAACGATGCCTACGCCGAGGGTGCCCTGGTGCTGGGCTCATCTCTGAC
ACAGCACAGGACCTCCCAAAGCCTGGCCGTGCTCACCGCCCCACACGTCTCAGACACCATGAGAAAGCCTTTAGACATAG
TCTCTGATGAAGTCACCACAGTGGACATCTTGGACAGTGGCGACTCTGCGCATCTCACCTTAATGAAGAGGCCCGAGTTG
GGTGTCGCACTGACCAAACTGCACTGCTGGTCCCTTACCCAGTATTCAAAATGTGTGTTCGTGGGTGCAGATACTCTGGT
TCTGGCAAATATTGATGCTGTTTTTGAGAGAGAACTGTCGGCTGCACCAGACCCAGGCTGGCCTGACCGCCTCAACCCTG
GGGTCTTTGTTTATCAGCCTTCGGTGGAAACCTATAATCAGCTGTTGCACGTTGCTTCCGAGCGAGGCAGTTTTGATGGT
GGGGACCAGGGCTTACTG

Alignment

ORF - retro_ocun_1766 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 50.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKDQAFVTLTTNDAYAKGALVLGSSLKQHRTSRRLAVLTTPQVSDTMRKALEIVFDEVITVDILDSGDSA
          M.DQAFVTLTTNDAYA.GALVLGSSL.QHRTS..LAVLT.P.VSDTMRK.L.IV.DEV.TVDILDSGDSA
Retrocopy MTDQAFVTLTTNDAYAEGALVLGSSLTQHRTSQSLAVLTAPHVSDTMRKPLDIVSDEVTTVDILDSGDSA

Parental  HLTLMKRPELGVTLTKLHCWSLTQYSKCVFMDADTLVLANIDDLFEREELSAAPDPGWPDCFNSGVFVYQ
          HLTLMKRPELGV.LTKLHCWSLTQYSKCVF..ADTLVLANID..FER.ELSAAPDPGWPD..N.GVFVYQ
Retrocopy HLTLMKRPELGVALTKLHCWSLTQYSKCVFVGADTLVLANIDAVFER-ELSAAPDPGWPDRLNPGVFVYQ

Parental  PSVETYNQLLHVASEQGSFDGGDQGLL
          PSVETYNQLLHVASE.GSFDGGDQGLL
Retrocopy PSVETYNQLLHVASERGSFDGGDQGLL

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	0.17 RPM	40.40 RPM
SRP017611_kidney	0.10 RPM	23.51 RPM
SRP017611_liver	0.08 RPM	5.01 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1766 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1766 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1766 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001467	2 retrocopies	retro_cjac_1049, retro_cjac_2915,
Danio rerio	ENSDARG00000011934	1 retrocopy	retro_drer_23,
Homo sapiens	ENSG00000163754	2 retrocopies	retro_hsap_1222, retro_hsap_159,
Myotis lucifugus	ENSMLUG00000006382	1 retrocopy	retro_mluc_2351,
Macaca mulatta	ENSMMUG00000005521	2 retrocopies	retro_mmul_1297, retro_mmul_376,
Nomascus leucogenys	ENSNLEG00000002557	2 retrocopies	retro_nleu_1556, retro_nleu_693,
Oryctolagus cuniculus	ENSOCUG00000003516	1 retrocopy	retro_ocun_1766 ,
Pongo abelii	ENSPPYG00000025899	2 retrocopies	retro_pabe_1015, retro_pabe_1080,
Pan troglodytes	ENSPTRG00000015509	1 retrocopy	retro_ptro_836,