RetrogeneDB ID: retro_ocun_625

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:120563391..120563695(+)
• Located in intron of: ENSOCUG00000014294

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013398
• Aliases: None
• Description: None

Sequence

>retro_ocun_625
ATGAGTAACACCACAGTGCCCAGTGCGCCCAGGCCAACAGTGACTCGATGGTGGGCTATGTGTTGGGCCCTTTCTTCCTC
ATCACCCTGGTCGGGGTGGTGGTGGCCGTGGTAATGTATGTCCAGAAGAGAAAACGGGTGGGCTGGCTTCGCCGCCACCT
GCTCCCACGTACAGCTATGACCCGGCTGAGGAGCTGCACGAGGCTGAGCAGGAGCTCCTGTCAGACGTGGGAGACCCGAA
GGTGGTGCATGGCTGGCAGGGTGGCTACCACCACAAGCGGGTGCCCCTGCTGGATGTCAAGACC

Alignment

ORF - retro_ocun_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSNTTVPNAP-QANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKRKRVDRLRHHLLPM-YSYDPAEELHE
          MSNTTVP.AP.QANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKRKRV..LR.HLLP..YSYDPAEELHE
Retrocopy MSNTTVPSAP<QANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKRKRVGWLRRHLLPR<YSYDPAEELHE

Parental  AEQELLSDVGDPKVVHGWQSGYQHKRVPLLDVKT
          AEQELLSDVGDPKVVHGWQ.GY.HKRVPLLDVKT
Retrocopy AEQELLSDVGDPKVVHGWQGGYHHKRVPLLDVKT

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	0.06 RPM	14.96 RPM
SRP017611_kidney	0.20 RPM	8.51 RPM
SRP017611_liver	0.00 RPM	1.23 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_625 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_625 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
Ailuropoda melanoleuca	ENSAMEG00000001058	1 retrocopy	retro_amel_1014,
Bos taurus	ENSBTAG00000034519	1 retrocopy	retro_btau_261,
Equus caballus	ENSECAG00000005108	3 retrocopies	retro_ecab_236, retro_ecab_474, retro_ecab_700,
Myotis lucifugus	ENSMLUG00000011876	1 retrocopy	retro_mluc_137,
Mus musculus	ENSMUSG00000062753	1 retrocopy	retro_mmus_1543,
Oryctolagus cuniculus	ENSOCUG00000013398	1 retrocopy	retro_ocun_625 ,
Pelodiscus sinensis	ENSPSIG00000004692	1 retrocopy	retro_psin_32,