RetrogeneDB ID: retro_ocun_885

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:10584119..10584554(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023468
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SYNJ2BP
• Ensembl ID: ENSOCUG00000008559
• Aliases: None
• Description: synaptojanin 2 binding protein [Source:HGNC Symbol;Acc:18955]

Sequence

>retro_ocun_885
ATGAACGGAAGAGTGGATTATTTAATCACCAAGGAAGAAACCAATCTTACCAGAGGACCCTCAGGGCTGGCCTTCAACAT
TGTCGGTGGGACAGATCAACAGTATGTCTCCAATGACAGTGGGATCTATGTCAGCCGCATCAAAGAGAATGGGGCTGCAG
CCCTGGATGGGCGGCTCCAGGAGGGTGATAAGATCCTCTCGGTAAATGGCCAGGACCTAAAGAACCTCCTGCATCAGGAT
GCTGTAGATCTCTTTCGTAACACAGGCTATGCTGTGTCCCTGAGAGTACAGCACAGGTTACAGGTGCAGAATGGACCTCT
TGCACATCGAGGTGAAGGGGAGCCAAGTGGCATTCCCATGGCTGTGGTTCTGGTGCCAGTGTTTGCCCTCACCATGGTGG
CAGCCTGGGCTTTCATGAGATACCGGCAACAGCTA

Alignment

ORF - retro_ocun_885 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGRVDYLITEEEINLTRGPSGLGFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNG
          MNGRVDYLIT.EE.NLTRGPSGL.FNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNG
Retrocopy MNGRVDYLITKEETNLTRGPSGLAFNIVGGTDQQYVSNDSGIYVSRIKENGAAALDGRLQEGDKILSVNG

Parental  QDLKNLLHQDAVDLFRNAGYAVSLRVQHRLQVQNGPLAHRGEGEPSGIPMAVVLVPVFALTMVAAWAFMR
          QDLKNLLHQDAVDLFRN.GYAVSLRVQHRLQVQNGPLAHRGEGEPSGIPMAVVLVPVFALTMVAAWAFMR
Retrocopy QDLKNLLHQDAVDLFRNTGYAVSLRVQHRLQVQNGPLAHRGEGEPSGIPMAVVLVPVFALTMVAAWAFMR

Parental  YRQQL
          YRQQL
Retrocopy YRQQL

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	20.25 RPM
SRP017611_kidney	0.00 RPM	35.98 RPM
SRP017611_liver	0.00 RPM	14.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_885 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_885 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_885 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007586	1 retrocopy	retro_btau_1114,
Cavia porcellus	ENSCPOG00000023967	1 retrocopy	retro_cpor_836,
Gorilla gorilla	ENSGGOG00000014492	1 retrocopy	retro_ggor_1470,
Mus musculus	ENSMUSG00000090935	3 retrocopies	retro_mmus_1428, retro_mmus_1538, retro_mmus_1802,
Oryctolagus cuniculus	ENSOCUG00000008559	1 retrocopy	retro_ocun_885 ,