RetrogeneDB ID: retro_ocun_695

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:47219484..47220156(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STOML2
• Ensembl ID: ENSOCUG00000006451
• Aliases: None
• Description: stomatin (EPB72)-like 2 [Source:HGNC Symbol;Acc:14559]

Sequence

>retro_ocun_695
ATGTTGGCGAGTGCGGAGCGGGACACTGGAGCCCTTTTGCTAAGGGGCTCTGTGCAGGGGTCTGTTGGAGCTCTGTGCCG
CGCCTCCTCTGGATTGCCCTGAAACACCGTGGTACTGTTTGTGCCTTAGCAGGAGGCCTGGGTGGTGGAGTGAATGGGCC
AATTCCACCGGATACTGGAGCCTGGCCTGAATATCCTCATCCCTGTGTTAGACCAGATCTGATATGTGCAGAGTCGCAAG
GAAATTGTCATCAATGTGCCAGAGCAGTCGGCTGTGACTGTTGGTGAGTGGGCAGACAATGTAACTCTGCAAATTGACAG
GGTCCTGTACCTGTGCATCATGGACCCTTACAAGGCAAGCTGTGGTGTGGAGGATCCTGAATATGCTGTCACCCAGCTAG
CTAGACAACCATGAGATCAGAGTTTTGCAAACTCTCCCTGGACTAAGTCTTCTGGGAGCAGGAGTCTCTGAATGCCAAAA
TTGTGGATACCATCAACCAGACTGCAGACTGCTGGGGCATCCGCTGCCTCCGTTATGAGATCAAGGATATCCATATGCCT
CCCCAGGTGAGAGTCCATGCAGATGCAGGTAGAGGCAGAGCGGCGAGAACGGGCCACAGTTCTAGAGTCGGAAGGGACCC
GGAAGTCTGCCATCAACGTGGTGAGGGCCCGT

Alignment

ORF - retro_ocun_695 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 62.08 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLARAARGTGALLLRGSVQASVRAPHRASSGLPRNTVVLFVPQQEAWVVERMGRFHRILEPGLNILIPVL
          MLA.A.R.TGALLLRGSVQ.SV.A..RASSGLP.NTVVLFVP.QEAWVVE.MG.FHRILEPGLNILIPVL
Retrocopy MLASAERDTGALLLRGSVQGSVGALCRASSGLP*NTVVLFVP*QEAWVVE*MGQFHRILEPGLNILIPVL

Parental  DRIRYVQSLKEIVINVPEQSAVTL----DNVTLQIDGVLYLRIMDPYKASYGVEDPEYAVTQLAQ-TTMR
          D.I.YVQS.KEIVINVPEQSAVT.....DNVTLQID.VLYL.IMDPYKAS.GVEDPEYAVTQLA..TTMR
Retrocopy DQI*YVQSRKEIVINVPEQSAVTVGEWADNVTLQIDRVLYLCIMDPYKASCGVEDPEYAVTQLAR<TTMR

Parental  SELGKLSLDKVFRERESLNANIVDAINQAADCWGIRCLRYEIKDIHVP-PRVKESMQMQVEAERRKRATV
          SE..KLSLD.VF.E.ESLNA.IVD.INQ.ADCWGIRCLRYEIKDIH.P.PR..ESMQMQVEAERR.RATV
Retrocopy SEFCKLSLD*VFWEQESLNAKIVDTINQTADCWGIRCLRYEIKDIHMP>PR*-ESMQMQVEAERRERATV

Parental  LESEGTRESAINVAEGK
          LESEGTR.SAINV....
Retrocopy LESEGTRKSAINVVRAR

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	46.63 RPM
SRP017611_kidney	0.00 RPM	76.83 RPM
SRP017611_liver	0.00 RPM	28.29 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_695 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_695 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_695 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000000485	1 retrocopy	retro_cint_6,
Callithrix jacchus	ENSCJAG00000009137	1 retrocopy	retro_cjac_440,
Ciona savignyi	ENSCSAVG00000000950	1 retrocopy	retro_csav_5,
Microcebus murinus	ENSMICG00000005517	1 retrocopy	retro_mmur_571,
Mus musculus	ENSMUSG00000028455	1 retrocopy	retro_mmus_1034,
Oryctolagus cuniculus	ENSOCUG00000006451	1 retrocopy	retro_ocun_695 ,