RetrogeneDB ID: retro_ocun_1103

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:77712798..77713199(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000025585
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000001108
• Aliases: None
• Description: None

Sequence

>retro_ocun_1103
GTGGTGGACCTACTGGGCTCCAATCGGAGCTCCCTGGAGAAACCACCCAGCCCCAGAGACCAGGAGATTTGGCGCAAGGC
CAGAGAGCAAGCTGCCCGCCTAAAGGATCTAAAAGACCAAGAGAAACAACAGAAACTAGAGTTTCATAAAAGGATGGAGA
AAGAGGTATCCTATTTCGTCCCAGACAGTGAGCAGATCACGGTACACTATGGGTCAATGAACAAGATTAGGAAGCAGCAT
CCTGCCCACCGTGGCGGAGGTGGCTGACCTGACATCCTTCCCCTCCAGGGAAGACAATGATTGGAGCTATGTCACGGTCC
TCAAAAAGGAGTTTGTACCCTCGGGTGAAGAGCTGGACTCCTACAGCCATGGAGAGCAAAGAGGACCCCCAGGAGGCTAA
A

Alignment

ORF - retro_ocun_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.96 %
• Parental protein coverage: 58.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADLLGSILSSMEKPPSLGDQETRRKAREQAARLKKLQEQDKQQKLEFRRRMEKEVSDFIQDSGQIKKKF
          ..DLLGS..SS.EKPPS..DQE..RKAREQAARLK.L..Q.KQQKLEF..RMEKEVS.F..DS.QI....
Retrocopy VVDLLGSNRSSLEKPPSPRDQEIWRKAREQAARLKDLKDQEKQQKLEFHKRMEKEVSYFVPDSEQITVHY

Parental  QPMNKIER-SILHDVVEVAGLTSFSFGEDDDCRYVMIFKKEFAPSDEELDSYRRGEE-WDPQKAE
          ..MNKI...SIL..V.EVA.LTSF...ED.D..YV...KKEF.PS.EELDSY..GE...DPQ.A.
Retrocopy GSMNKIRK>SILPTVAEVADLTSFPSREDNDWSYVTVLKKEFVPSGEELDSYSHGEQ>EDPQEAK

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	77.54 RPM
SRP017611_kidney	0.00 RPM	64.87 RPM
SRP017611_liver	0.00 RPM	33.45 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1103 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006299	1 retrocopy	retro_amel_964,
Canis familiaris	ENSCAFG00000015761	1 retrocopy	retro_cfam_1417,
Dasypus novemcinctus	ENSDNOG00000011669	1 retrocopy	retro_dnov_1149,
Echinops telfairi	ENSETEG00000020098	1 retrocopy	retro_etel_1489,
Felis catus	ENSFCAG00000030469	1 retrocopy	retro_fcat_833,
Macropus eugenii	ENSMEUG00000007933	1 retrocopy	retro_meug_1358,
Myotis lucifugus	ENSMLUG00000014031	1 retrocopy	retro_mluc_1561,
Mus musculus	ENSMUSG00000018287	1 retrocopy	retro_mmus_2553,
Oryctolagus cuniculus	ENSOCUG00000001108	1 retrocopy	retro_ocun_1103 ,