RetrogeneDB ID: retro_cpor_1525

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_93:3042210..3042958(+)
• Located in intron of: ENSCPOG00000008205

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTBP2
• Ensembl ID: ENSCPOG00000008397
• Aliases: None
• Description: None

Sequence

>retro_cpor_1525
GGGCAAGCGGCTGCTGTTTAAGCCAAGGCCTTTGGATTCAGCATCATGTTTCATGACCCCTACTTGCAGGATGGCATAGA
ACGATCCCTGGGTGTGCAGAGGGTCTACACCTTACAGGATTTGCTGTATCAGAGTGACTGTGTCTCCTTGCACTGCAATC
TCAATGAATATAACCACCACCTCATCAGTGACTTTACCATAAAGTAGATGAGGCAAAGAGCACTCCTAGTGAATGCAGCC
CGAAGTGGCCTGGCAGATGAGAAAGCCTTAGCCCAGATCTTCAAAGAGGGCAGGATACGAGGGGCAGCCCTTTATGTGTA
CAAATCTGAGCCCTTTAGCTATGCTCAGAGTCCACTGAAAGATGCACCAAATCTCATCTGTACTCCCCACACAGCCTGGC
ACAATGAACAAGCATCCCTGGAGATGAGGAAGACAGCTGCTATAGAGATCCACCAAGTGATCACAGGTCGCATCCCAGAA
AGATTAAGAAACTGTGTCAATAAGGAATTCTTCATCACATCAGCTCTATGGTCAGCAATAGACCAGCAGCAATTCATCCT
GAGCTCGGTGGTGCCACATACAAGTATCCACCAGGTGTGGCTCCAGGAGGACTCATTGCAGCCATGGAAGGGATTATTCC
AGTAGGCATCCCAGTGATTCCCAACTTCCCCATGGTGGCACATCCTTCCCAAGCCCCCTTTCCCAACCAGTCCACAAAAC
ACGGGACAATCGAGAGCACCCCAACGAG

Alignment

ORF - retro_cpor_1525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.57 %
• Parental protein coverage: 59.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQAVAVRAKAFGFSVIFYDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEHNHHLINDFTIKQM
          GQA.AV.AKAFGFS..F.DPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNE.NHHLI.DFTIK.M
Retrocopy GQAAAV*AKAFGFSIMFHDPYLQDGIERSLGVQRVYTLQDLLYQSDCVSLHCNLNEYNHHLISDFTIK*M

Parental  RQGAFLVNAARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFAQGPLKDAPNLICTPHTAWYSEQASL
          RQ.A.LVNAAR.GL.DEKALAQ..KEGRIRGAAL.V..SEPFS.AQ.PLKDAPNLICTPHTAW..EQASL
Retrocopy RQRALLVNAARSGLADEKALAQIFKEGRIRGAALYVYKSEPFSYAQSPLKDAPNLICTPHTAWHNEQASL

Parental  EMREAAATEIRRAITGRIPESLRNCVNKEFFVTSAPWSVIDQQ-AIHPELNGATYRYPPGIVGVAPGGLP
          EMR..AA.EI...ITGRIPE.LRNCVNKEFF.TSA.WS.IDQQ.AIHPEL.GATY.YPPG...VAPGGL.
Retrocopy EMRKTAAIEIHQVITGRIPERLRNCVNKEFFITSALWSAIDQQ<AIHPELGGATYKYPPG---VAPGGLI

Parental  AAMEGILPGGIPVTHNLPTVAHPSQAPSPNQPTKHG-DNREHPNE
          AAMEGI.P.GIPV..N.P.VAHPSQAP.PNQ.TKHG.DNREHPNE
Retrocopy AAMEGIIPVGIPVIPNFPMVAHPSQAPFPNQSTKHG<DNREHPNE

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	12.19 RPM
SRP017611_kidney	0.00 RPM	23.14 RPM
SRP017611_liver	0.00 RPM	3.87 RPM
SRP040447_lung	0.03 RPM	38.76 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1525 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1525 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012539	2 retrocopies	retro_cjac_1866, retro_cjac_2528,
Cavia porcellus	ENSCPOG00000008397	1 retrocopy	retro_cpor_1525 ,
Oryctolagus cuniculus	ENSOCUG00000007076	1 retrocopy	retro_ocun_378,
Otolemur garnettii	ENSOGAG00000024152	2 retrocopies	retro_ogar_1393, retro_ogar_45,