RetrogeneDB ID: retro_cpor_546

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:16954424..16955123(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BMI1
• Ensembl ID: ENSCPOG00000015427
• Aliases: None
• Description: None

Sequence

>retro_cpor_546
ATGCATGGAACAGCCAGAGTCAAGAGCACTGAGCTCAGTCCCCAAATTGTGTGTGTGCTTGTGGAGGGCACTTCACTGAT
GCCACAGCCATCACAGGATGCCCACATCCCTTCTGTAAAATGTGTATTGTGCGTTGCCTGGAGTCCAGCAAGTATTGTCC
TATCTGTGATGTCCAAGTTCACAACACCAGACACCACTGAGTATAAGGTCAGATAAAACACTTAAAGATATCATGTACAA
ATTAGTCCCAGGGCTTTTCAAAAATGAAATGAAGAGAAGGATGCATTTTTATGCAGCTCATCCTTCAGCTGATGCCAGTG
GCTCTAATGAAGATAAAGAAATTGGAGATGAAAAGAAGGGGATTATAACTGACAGAGGGATAATAAGCTTATCCATTGAA
TTATTTGACCAGAATAGATTGGACGAGAAAGTAACAAAGACAAACAGAAGTCTAAGGAGGTGGTGAATGATAAAAGATAT
TTACGATGCCCAGCAGCATTGACTGTGATGCACTTAAGAGAGTTTCTCAGAAGTAAAATGGATACACCTGATACTCTCCA
GACCGATGTCATGTATGATGACAAACCTTTAAAGGATTACGATCTACTAATGGACATTGCCTACATTTATACCTGGAGAA
GGAATGGTCCACTTACTTTGAAATACAGAGTTCGACCAACTTGTAAGAGAAAGAAGATC

Alignment

ORF - retro_cpor_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.57 %
• Parental protein coverage: 72.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MHRTTRIKITELNPHLMCVL-CGGYFIDATTIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTR-PLLN
          MH.T.R.K.TEL.P...CVL.CGG.F.DAT.I..C.H.FCK.CIVR.LE.SKYCPICDVQVH.TR...L.
Retrocopy MHGTARVKSTELSPQIVCVL<CGGHFTDATAITGCPHPFCKMCIVRCLESSKYCPICDVQVHNTR<TPLS

Parental  IRSDKTLQDIVYKLVPGLFKNEMKRRRDFYAAHPSADAANGSNEDRGEVADEEKRIITDDEIISLSIEFF
          IRSDKTL.DI.YKLVPGLFKNEMKRR..FYAAHPSADA..GSNED..E..DE.K.IITD..IISLSIE.F
Retrocopy IRSDKTLKDIMYKLVPGLFKNEMKRRMHFYAAHPSADAS-GSNEDK-EIGDEKKGIITDRGIISLSIELF

Parental  DQNRLDRKV-NKDKEKSKEEVNDKRYLRCPAAMTVMHLRKFLRSKMDIPNTFQIDVMYEEEPLKDYYTLM
          DQNRLD.KV.NKDK.KSKE.VNDKRYLRCPAA.TVMHLR.FLRSKMD.P.T.Q.DVMY...PLKDY..LM
Retrocopy DQNRLDEKV<NKDKQKSKEVVNDKRYLRCPAALTVMHLREFLRSKMDTPDTLQTDVMYDDKPLKDYDLLM

Parental  DIAYIYTWRRNGPLPLKYRVRPTCKRMKI
          DIAYIYTWRRNGPL.LKYRVRPTCKR.KI
Retrocopy DIAYIYTWRRNGPLTLKYRVRPTCKRKKI

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	28.01 RPM
SRP017611_kidney	0.00 RPM	17.80 RPM
SRP017611_liver	0.00 RPM	12.45 RPM
SRP040447_lung	0.00 RPM	23.96 RPM
SRP040447_skeletal_muscle	0.00 RPM	21.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_546 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_546 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,