RetrogeneDB ID: retro_cpor_84

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:22608450..22610961(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004934
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005745
• Aliases: None
• Description: None

Sequence

>retro_cpor_84
CTCGGCGCCGTCGTCGGCGTGAAAATGGCGGCATCTATGGCGGCGGCGGCCTCTGCCACCTCGGGTAGCGCGAGCTCCGG
GGAGGGCTCAGCCGGTGGCGAGAATCGCGCGGCCGCCTCCTCGGCTGCAGCCTCAGCCTCGTCGCCCACGGCGGGCGGCG
GCGAGGCCCTGGAGCTGCTGGAACGCTGTGGAGCGTGCCGGGAGCGTCTGCGTCCAGAGCGCGAGCCGCGCCTGCTGCCT
TGCCTGCACTCGGCCTGCAGCGCCTGCCTCGCGCCCTCCGCGGCCAACAGCACCGGGGACGGTGGCCCGGCAGGCGACGG
CGCGGTGGTGGATTGCCCCGTGTGCAAACAGCAGTGCTGCTTCAAAGACATCGTGGAGAACTACTTTGTCCGCGACAGTG
GCAACAAGGCCGCCTCAGACGCCCAGGAGGCGAATCAGTGCTGCACTAGTTGCGAAGATAACGCGCCAGCCACCAGCTAT
TGCGTGGAGTGTTCCGAGCCACTGTGCGAGACCTGCGTGGAAGCTCACCAGCGGGTGAAGTACACCAAGGACCACACGGT
GCGTCCCACCGGGCCGGCCAAGTCCCGGGATGGAGAACGCACAGTCTACTGTAATGTGCACAAGCGGGAACCTCTCGTGC
TGTTCTGCGAGAGCTGCGACACCCTTACTTGTCGGGATTGCCAGCTCAGCGCCCACAAGGACCATCAGTACCAGTTCCTG
GAAGATGCCGTGAGGGACCAGCGCAAGCTCCTGGCCGCACTGGTGAAACGCCTTGGAGACAAACATGCCACGCTGCAGAA
GAGCACCAAGGAGGTTCGAAGCTCCATCCGCCAGGTGTCCGATGTGCAGAAACGAGTGCAGGTGGATGTTAAGATGGCCA
TCTTGCAGATCATGAAGGAGCTGAACAAGCGGGGCCGCGTGCTGGTCAGCGATGCGCAGAAGTTGACGGAGGGGCAGCAG
GAACGCCTGGAACGGCAGCACTGGTCCATGACCAAGATCCAGAAGCACCAGGAACACATCTTGCGCTTTGCCTCTTGGGC
TCTAGAGAGTGATAACAACACAGCTCTGCTGCTGTCTAAGAAGCTCATCTACTTCCAGCTGCAGCGAGCCCTCAAGATGA
TCGTGGAACCCGTGGAGCCCCACGGGGAGATGAAGTTCCAGTGGGACCTCAGTGCCTGGACCAAGAGTGCGGAGGCCTTC
GGTAAGATTGTCGCTGAGCGTCCTGGTACTAACTCCACGGGCCCTGCACCCATGGCTCCCCCGAGAGCCCTGGGACCCCT
GAGCAAGCAGAGTTCTAGCAGTAGCCAGCCCATGGAAGTCCAGGAAGGTTATGGCTGTGAATCAGATGACCCCTACTCCA
GTGCAGAGCCCCATGTGTCGGGCATGAAGCGATCCTCCTCTGGTGAGGGCGAGGTGAGTGGCCGCATGCGCAAGGTGCCA
CGGGTGAGCCTCGAACGCCTGGACCTGGACCTTACAGGCGACAGCCAGCCACCAGTCTTCAAGGTCTTTCCAGGCACCAC
CACTGAGGACTACAACCTCATTGTTATTGAGCGTGGTGGTGCTGCTGCCGCAGCTGCTGGTCAACCTGGGACTGCGCCCC
CTGGAGCAGCCGGCGCTCCACCCCTTCCCAGCATGGCCATTGTGAAGGAGGAGGAGATGGAGGCTGCCATTGGAGCTCCT
CCTGCTGCTGCCGTCGCCCCAGCCGCCATGGAAGGCCCTGAGACCAAGCCTGTGCTCATGGCTCTGGCTGAAGGCCCTGC
CGCAGAGGGCCCCCGCCTGGCTTCACCTAGTGGCAGCACTAGCTCAGGCCTGGAGGTGGTGGCTCCCGAGGGTAGCACAG
CACCAGGTGGTGACCCAGGCACCTTGGATGACAGCGCCACCATCTGCCGTGTCTGCCAAAAGCCAGGTGACCTGGTCATG
TGCAACCAGTGCGAGTTTTGCTTCCACCTGGACTGCCACCTGCCCGCCCTGCAGGATGTGCCAGGGGAGGAGTGGAGCTG
CTCGCTCTGCCACGTGCCCCCTGAGCTAAAGGAGGAGGATGGCACCCTCAGCATGGATGGAGCAGACAGCACCGGCATAG
TGGCCAAGCTCTCGCCCATCAACCAGCAGAAATGCGAACGCGTCCTGCTGGCCCTCTTCTGCCACGAACCGTGCCGCCCC
CTGCACCAGCTGGCCACCGACTCTCCCTTCTCCATGGAGCAGCCAGGCGGCACCCTGGACTTGACCCTGATCCGTGCCCG
CCTCCAGGAAAAGTTGTCACCCCCTTACAGCTCCCCCCAGGAGTTTGCTGAGGATGTGGGCCGCATGTTCAAGCAGTTTA
ACAAGCTGACTGAGGACAAGGCGGATGTGCAGTCTATCATCGGTCTTCAGCGCTTCTTCGAGTCACGCCTGAACGAGGCC
TTTGGCGACACCAAGTTCTCTGCTGTCCTGGTGGAGCCCCCGCCACTGAGCCTGCCCGGCGCTGGTCCTAGTTCCCAGGA
GCTGTCTGGTGGTCCTAGTGATGGTCCCTAA

Alignment

ORF - retro_cpor_84 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.57 %
• Parental protein coverage: 67.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALCPSSPSPGGSPGPAEGSAGGEKSAGAAAAAASASASASSPSGSGDEALELLEHCGLCRERLLPEREPR
          ..........GS....EGSAGGE......AAA.SA.ASASSP...G.EALELLE.CG.CRERL.PEREPR
Retrocopy SMAAAASATSGSASSGEGSAGGENR----AAASSAAASASSPTAGGGEALELLERCGACRERLRPEREPR

Parental  LLPCLHSACSSCLGPTAPAAANNAGDGPAASDNTMVDCPVCKQQCSSKDIVENYFMRDSGNKAASDAQDA
          LLPCLHSACS.CL...AP.AAN..GDG..A.D...VDCPVCKQQC..KDIVENYF.RDSGNKAASDAQ.A
Retrocopy LLPCLHSACSACL---APSAANSTGDGGPAGDGAVVDCPVCKQQCCFKDIVENYFVRDSGNKAASDAQEA

Parental  NQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRSTGPAKSRDGERTVYCTVHKHEPLVL
          NQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVR.TGPAKSRDGERTVYC.VHK.EPLVL
Retrocopy NQCCTSCEDNAPATSYCVECSEPLCETCVEAHQRVKYTKDHTVRPTGPAKSRDGERTVYCNVHKREPLVL

Parental  FCESCDTLTCRDCQLNAHKDHKYQFLEDAVRNQRKVLVSMVKCLGDRHATLQKSTKEVWSSIRQVSDVQK
          FCESCDTLTCRDCQL.AHKDH.YQFLEDAVR.QRK.L...VK.LGD.HATLQKSTKEV.SSIRQVSDVQK
Retrocopy FCESCDTLTCRDCQLSAHKDHQYQFLEDAVRDQRKLLAALVKRLGDKHATLQKSTKEVRSSIRQVSDVQK

Parental  RVQVDVKMAILQIMKELNKRGRVLVNDAQKVTEGQQERLERQHWALTKIQKHQEHILRFASWALKSDNNT
          RVQVDVKMAILQIMKELNKRGRVLV.DAQK.TEGQQERLERQHW..TKIQKHQEHILRFASWAL.SDNNT
Retrocopy RVQVDVKMAILQIMKELNKRGRVLVSDAQKLTEGQQERLERQHWSMTKIQKHQEHILRFASWALESDNNT

Parental  ALLLSKKLIYFQLHRALKMIVDPVEPHGEMKFQWDLNAWTKSAEAFGKIVAERPGTNSTGPAPMAPPRAP
          ALLLSKKLIYFQL.RALKMIV.PVEPHGEMKFQWDL.AWTKSAEAFGKIVAERPGTNSTGPAPMAPPRA.
Retrocopy ALLLSKKLIYFQLQRALKMIVEPVEPHGEMKFQWDLSAWTKSAEAFGKIVAERPGTNSTGPAPMAPPRAL

Parental  GPLSKQGSSSSQPMEVQEAYGFGSADNPYSSAEPHVSGMKRSRSGEGEVSGLMRKVPRVSLERLDLDLTA
          GPLSKQ.SSSSQPMEVQE.YG..S.D.PYSSAEPHVSGMKRS.SGEGEVSG.MRKVPRVSLERLDLDLT.
Retrocopy GPLSKQSSSSSQPMEVQEGYGCES-DDPYSSAEPHVSGMKRSSSGEGEVSGRMRKVPRVSLERLDLDLTG

Parental  DSQPPVFKVFPGSTTEDYNLIVIERGG-AAAAAGQPGTAPPGVPGAPPLPGMAIVKEEETEAAIGAPPPA
          DSQPPVFKVFPG.TTEDYNLIVIERGG.AAAAAGQPGTAPPG..GAPPLP.MAIVKEEE.EAAIGAPP.A
Retrocopy DSQPPVFKVFPGTTTEDYNLIVIERGGAAAAAAGQPGTAPPGAAGAPPLPSMAIVKEEEMEAAIGAPPAA

Parental  TEVP
          ...P
Retrocopy AVAP

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	46.36 RPM	81.33 RPM
SRP017611_kidney	60.72 RPM	90.35 RPM
SRP017611_liver	20.50 RPM	47.14 RPM
SRP040447_lung	76.29 RPM	131.85 RPM
SRP040447_skeletal_muscle	46.77 RPM	76.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_84 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_84 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005745	1 retrocopy	retro_cpor_84 ,
Procavia capensis	ENSPCAG00000007149	1 retrocopy	retro_pcap_462,