RetrogeneDB ID: retro_ocun_443

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:14817503..14817821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VMA21
• Ensembl ID: ENSOCUG00000015201
• Aliases: None
• Description: VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:22082]

Sequence

>retro_ocun_443
TGCCTGCACCGCCAAGCCGTGGAGCACCATGATCAGTCACAGCAGAACGTGCTGCAGCCGCTGGAGTTGAGAAGCGAGAA
GTCCTCAACCTCCACCCTGAGACTCGCGTGTTCCTCACTGCTTTAATGATAACTGTGCCTACTGCCTTCTGCTTCACAAC
GGAATCTTACGTATTTGAAGGTGCCCTGGGGCTGTGCAGTGGGACAGCTGGTTTTACGCGGCCATTGCTGCATGGTGGCG
GTCCACGTGGTGCTGGCCCTCTTTGTGTATGGGGCCTGGAATGAGGACTCGCGACAGTGGCGTGAAGGCAAGCAGGAT

Alignment

ORF - retro_ocun_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.36 %
• Parental protein coverage: 70.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CRHRDAMERLDKAALNALQPPEFRSENSLASTLK-TLLFFTALMITVPIGLYFTTKSYIFEGALGMSNR-
          C.HR.A.E..D....N.LQP.E.RSE.S..STL..T..F.TALMITVP....FTT.SY.FEGALG.....
Retrocopy CLHRQAVEHHDQSQQNVLQPLELRSEKSSTSTLR<TRVFLTALMITVPTAFCFTTESYVFEGALGLCSG<

Parental  DSYFYAAIVA-VVAVHVVLALFVYVAWNEGSRQWREGKQD
          DS.FYAAI.A..VAVHVVLALFVY.AWNE.SRQWREGKQD
Retrocopy DSWFYAAIAA<MVAVHVVLALFVYGAWNEDSRQWREGKQD

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	3.26 RPM
SRP017611_kidney	0.00 RPM	6.28 RPM
SRP017611_liver	0.00 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_443 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_443 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_443 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443 ,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,