RetrogeneDB ID: retro_ocun_1849

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019335:12537..12941(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021384
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSOCUG00000004488
• Aliases: None
• Description: glia maturation factor, beta [Source:HGNC Symbol;Acc:4373]

Sequence

>retro_ocun_1849
GTGAGTGAGTCTTTGGTGGTTTGTGATGTGGCTGAAGATTTACTGGAAAAGCTGAGGAAGTTTCATTTTCACAAAGAAAC
AATTGATGCTGCCATTATAATGAAGATTGAGAAAGATAAACACTTGGTGGTACTGGATGAGGAACTTGAGGGCATTTCTC
CGGATGAACTTAAGGATGAGCTACCTGAGCGACAGCCTCGCTTCATTGTGTATAGTTCCAAATATCAACATGATGATGAA
GAGTGTCGCATCCTCCGTGCTTTATTTTCTCCGGTCTTGTTGGATGTAAGCCTGAGCAGCAGGTGATGTATGCTGGAAGT
AGGAATAAGCTAGTGCAGACAGCTGAGCTGCCCAAGGTATTTGAAATAAGAAATACTGAAGACCTACCTGAAGAGTGGTT
ACGT

Alignment

ORF - retro_ocun_1849 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.67 %
• Parental protein coverage: 95.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSESLVVCDVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGVSPDELKDELPERQPRTFI
          .SESLVVCDVAEDL.EKLRKF.F.KET..AAIIMKI.KDK.LVVLDEELEG.SPDELKDELPERQPR.FI
Retrocopy VSESLVVCDVAEDLLEKLRKFHFHKETIDAAIIMKIEKDKHLVVLDEELEGISPDELKDELPERQPR-FI

Parental  VYSYKYQHDDG-RVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWLR
          VYS.KYQHDD..RVS.P.CFIFS..VGCKPEQQ.MYAGS.NKLVQTAEL.KVFEIRNTEDL.EEWLR
Retrocopy VYSSKYQHDDE<RVSHPPCFIFSGLVGCKPEQQVMYAGSRNKLVQTAELPKVFEIRNTEDLPEEWLR

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	208.00 RPM
SRP017611_kidney	0.00 RPM	68.21 RPM
SRP017611_liver	0.00 RPM	33.14 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1849 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1849 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1849 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007312	1 retrocopy	retro_cjac_736,
Cavia porcellus	ENSCPOG00000004207	1 retrocopy	retro_cpor_240,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849 , retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,