RetrogeneDB ID: retro_ocun_347

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:19859337..19859756(-)
• Located in intron of: ENSOCUG00000002573

Retrocopy information

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

Parental gene information

• Parental gene symbol: IRAK1BP1
• Ensembl ID: ENSOCUG00000001488
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 1 binding protein 1 [Source:HGNC Symbol;Acc:17368]

Sequence

>retro_ocun_347
GGGACCAGAAGAATGTGGTCTCAAGAGGCACCGCCCGTTGGCCATACCCCCCTGTCCTGTGCACAAACTCAGACTCCAAA
CTGCGACCTACAAGGTGGCAGCACAGAGAGTTCTGCAGGACCAGACCCGGCCAAGTGGCAGGAGCAGTGAGCAGCACCAA
GGAGGCTATGGCGGAAGCCAAGATCGTTTACCAACACCTGGACTCTGTCAAGTAGAGTCTGGAGCAGTGAGGTCTGCAGA
CAGAAATAACTGCTACAAAGGATTTCAGAAGAGTAGAAAATGTGTATCACGTAAAAGCAGAGGACTGTATTACATTTACT
GAAATTGGAAAAATGTAAAATATCTTTGACTTCCTTGTTGGAAAGCGAGATAGCTCTGTTGTCATAAGCCCACCCCACAG
CTGTAAGACTCCAGGTGCA

Alignment

ORF - retro_ocun_347 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.33 %
• Parental protein coverage: 55.43 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRENVVSGETLPGVRRPLSSTQTQTATREVHVSGTAEVSAGPDRA-QVAVRVSSTKEAAAEAKKSVCRRL
          G.....S.E..P....PLS..QTQT........G..E.SAGPD.A.QVA..VSSTKEA.AEAK..V...L
Retrocopy GTRRMWSQEAPPVGHTPLSCAQTQTPNCDLQ-GGSTESSAGPDPA<QVAGAVSSTKEAMAEAK-IVYQHL

Parental  DYITQSLQQRGLQTENVTVTKDFRRVENAFHMEAEVCITFTEFGKMQNICNFLVEKLDSSVVISPPQFYH
          D....SL.Q.GLQTE..T.TKDFRRVEN..H..AE.CITFTE.GKM.NI..FLV.K.DSSVVISPP....
Retrocopy DSVK*SLEQ*GLQTE-ITATKDFRRVENVYHVKAEDCITFTEIGKM*NIFDFLVGKRDSSVVISPPHSCK

Parental  TPGS
          TPG.
Retrocopy TPGA

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	5.30 RPM
SRP017611_kidney	0.41 RPM	5.98 RPM
SRP017611_liver	0.00 RPM	0.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_347 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_347 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_347 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012945	1 retrocopy	retro_amel_783,
Canis familiaris	ENSCAFG00000002793	1 retrocopy	retro_cfam_429,
Monodelphis domestica	ENSMODG00000018444	1 retrocopy	retro_mdom_1885,
Oryctolagus cuniculus	ENSOCUG00000001488	1 retrocopy	retro_ocun_347 ,