RetrogeneDB ID: retro_ocun_489

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:85406088..85406676(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000008816
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000005420
• Aliases: None
• Description: None

Sequence

>retro_ocun_489
ATGCATTGAACAACCAGAATCAAGATCACTGAGCTACATCCCCACCTAATGTGTGTGCTTTGTGGAGGATACTTCATTGA
TGCCACCACCCTAATAGAATGTCTACATTCCTTCTGTAAAACATGTATTGTGCGTTACCCGGAGACCAGCAAGTATTGTC
CTATCTGTGATGTTCAAGCTCACAAAACCAGACCACTACTGAATATAAGGTCAGATAAAACTCTTCAAGATATCGTATAC
AAATTAGTTCCAGGGCTTTTCAAAAATGAAATGAAGAGAAGAAGGGATTTTTATGCAGCTCATCCTTCAGCTGATGCTGC
CAATGGCTCTAATGAAGATAGAGGAGAAGTTGCAGATGAAGATAAGAGAATTATAACTGATGATGAAATAATAAGTTTAT
CCATTGACTTCTTTGACCAGAACAGATTGGATCGGAAAGTAAGCAAAGATAAAGAGAAATCTAAGGAGCAGGTGAATGAT
AAAAGGTATTTACGATGCCCAGCAGCAATGACTATGACGCACTTAAGAAAGTTTCTCAGAAGTAGAATGGACATACCTAA
CACTCTCCAGACTGATGGCATGTATGAA

Alignment

ORF - retro_ocun_489 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHRTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIR
          MH.TTRIKITEL.PHLMCVLCGGYFIDATT.IECLHSFCKTCIVRY.ETSKYCPICDVQ.HKTRPLLNIR
Retrocopy MH*TTRIKITELHPHLMCVLCGGYFIDATTLIECLHSFCKTCIVRYPETSKYCPICDVQAHKTRPLLNIR

Parental  SDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIEFFDQ
          SDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSI.FFDQ
Retrocopy SDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEDKRIITDDEIISLSIDFFDQ

Parental  NRLDRKVSKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYE
          NRLDRKVSKDKEKSKE.VNDKRYLRCPAAMT..HLRKFLRS.MDIPNT.Q.D.MYE
Retrocopy NRLDRKVSKDKEKSKEQVNDKRYLRCPAAMTMTHLRKFLRSRMDIPNTLQTDGMYE

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	0.17 RPM	20.47 RPM
SRP017611_kidney	0.00 RPM	21.79 RPM
SRP017611_liver	0.08 RPM	2.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_489 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_489 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_489 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011962	1 retrocopy	retro_chof_709,
Callithrix jacchus	ENSCJAG00000036548	1 retrocopy	retro_cjac_2437,
Cavia porcellus	ENSCPOG00000015427	2 retrocopies	retro_cpor_1209, retro_cpor_546,
Gorilla gorilla	ENSGGOG00000025243	1 retrocopy	retro_ggor_3025,
Loxodonta africana	ENSLAFG00000016845	1 retrocopy	retro_lafr_591,
Macaca mulatta	ENSMMUG00000000881	1 retrocopy	retro_mmul_2591,
Mus musculus	ENSMUSG00000026739	1 retrocopy	retro_mmus_3710,
Oryctolagus cuniculus	ENSOCUG00000005420	1 retrocopy	retro_ocun_489 ,
Tupaia belangeri	ENSTBEG00000015631	1 retrocopy	retro_tbel_2369,