RetrogeneDB ID: retro_ocun_1697

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018780:514757..515682(-)
• Located in intron of: ENSOCUG00000004774

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSOCUG00000005230
• Aliases: None
• Description: protein phosphatase 2, catalytic subunit, beta isozyme (PPP2CB), mRNA [Source:RefSeq mRNA;Acc:NM_001101707]

Sequence

>retro_ocun_1697
ATGGACGACAAGACGTTCACCAAGGAGCTGGACCAGTGGGTCGAGCAGCTGAACGAGTGTAAACAGCTCAACGAGAACCA
AGTGCGGACGCTGTGCGAGAAGGCTAAGGAAATTTTAACAAAAGAATCCAATGTGCAAGAGGTTCGTTGTCCTGTTACCG
TCTGTGGAGATGTGCATGGTCAATTCCATGACCTTATGGAACTCTTTAGAATTGGTGGGAAACCACCGGATATAAACTAT
CTATTCATGGGAGACTAGGTGGACAGAGGTTATTACTCAGTGGAGACTGTGACTCTTCTTGTAGCATTAAAGGTGCGTTA
TCCAGAACACATTACAGTATTGAGAGGAAATCATGAAAGCCGACAAATTACCCAAGTATATGGCTTTTATGATGAATGTC
TACGGAAGCATGGAAATGCCAATGTGTGGAAATATTTTACAGACCTATTTGATTATCTTCCACTTACAGCTTTGGTAGAT
GGACAGATATTCTGCCTCCATGGTGGCCTGTCTCCATCCATAGATACACTGGATCATATAAGAGCCCTGGATGGTTTACA
AGAAGTTCCACACGAGGGCCCAACGTGTGATCTGTTGTGGTCTGATTCAGATGATCGTGGTGGGTGGGGTATTGCACCAC
GTGGTGCCGGCTACACTTTTGGACAAGACATTTCTGAAACATTTAACCACGCCAATGGTCTCACACTGGTCTCCCGTGAC
CACCAGCTTGTGCTGGAGGGATACAACTGGTGTCATGACCGGAATGTGGTTACCATTTTCAGTACACCTAATTACTGTTA
CCGTTGTGGGAACCAGGCTGCTATCATGGAATTAGATGACACTTTAAAATATTCCTTGTTCAGTTCGATCCAGCACCTCG
TCGTGGAGAGCCTCACGTAACCCGCGCACCCCAGACTACTTCCTG

Alignment

ORF - retro_ocun_1697 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDDKTFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
          MDDKTFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR
Retrocopy MDDKTFTKELDQWVEQLNECKQLNENQVRTLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFR

Parental  IGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYPERITILRGNHESRQITQVYGFYDECLRKYGNA
          IGGK.PD.NYLFMGD.VDRGYYSVETVTLLVALKVRYPE.IT.LRGNHESRQITQVYGFYDECLRK.GNA
Retrocopy IGGKPPDINYLFMGD*VDRGYYSVETVTLLVALKVRYPEHITVLRGNHESRQITQVYGFYDECLRKHGNA

Parental  NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWG
          NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALD.LQEVPHEGP.CDLLWSD.DDRGGWG
Retrocopy NVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDGLQEVPHEGPTCDLLWSDSDDRGGWG

Parental  ISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDD
          I.PRGAGYTFGQDISETFNHANGLTLVSR.HQLV.EGYNWCHDRNVVTIFS.PNYCYRCGNQAAIMELDD
Retrocopy IAPRGAGYTFGQDISETFNHANGLTLVSRDHQLVLEGYNWCHDRNVVTIFSTPNYCYRCGNQAAIMELDD

Parental  TLKYS-FLQFDPAPRRGEPHVTR-RTPDYFL
          TLKYS...QFDPAPRRGEPHVTR.RTPDYFL
Retrocopy TLKYS<LVQFDPAPRRGEPHVTR<RTPDYFL

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	1.38 RPM	109.55 RPM
SRP017611_kidney	3.95 RPM	63.25 RPM
SRP017611_liver	0.15 RPM	19.35 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1697 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1697 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012460	1 retrocopy	retro_cjac_985,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Homo sapiens	ENSG00000104695	1 retrocopy	retro_hsap_1631,
Gorilla gorilla	ENSGGOG00000013978	1 retrocopy	retro_ggor_380,
Macaca mulatta	ENSMMUG00000020819	1 retrocopy	retro_mmul_484,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Oryctolagus cuniculus	ENSOCUG00000005230	1 retrocopy	retro_ocun_1697 ,
Pongo abelii	ENSPPYG00000018491	1 retrocopy	retro_pabe_335,