RetrogeneDB ID: retro_cpor_518

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_18:7647430..7647899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DR1
• Ensembl ID: ENSCPOG00000003282
• Aliases: None
• Description: None

Sequence

>retro_cpor_518
TCCTCGCCTGACAACACTGATGATCATGCCATCCCCAGAGCTGCTATCAGTAAGACGATCAAAGGGGCTCTTCCCAATGC
CCAGTGGCCAGCAATGCCCGAGAGCTGGTGGTAAACTGCTGCACCGAACTCACTCACCTTATATCATCTGAAGCCAGTGA
GATTTGTAATACATCAGAAAAGAAGACGGTCTCCCCGGAGCACACCTTACAAGCCCTAGGAAGTTTGGGCTTTGGCTTGT
ACATCAGTGCAGTAAAAGAAGTCTTACAAAAATGCAAGATGGTAGCATTAGAAAGAAGAAAGGCCAGTTCTCATCTGGAA
AACCCTGGCATTCCTGAAGAAGGGTAACTGAGCCGGCAACAGGAATTATGCACAAAAGCTAAACAGCAACAAGCAGAACT
GGCCCCACAGGACTGGCTTCCAGTGCAGCGGGTGCCCAGCAAGCACGGCTCGCTGCTGCCTCGGCCAGC

Alignment

ORF - retro_cpor_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.7 %
• Parental protein coverage: 89.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SSSGNDDDLTIPRAAINKMIKETLPNVR-VANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHV
          SS..N.DD..IPRAAI.K.IK..LPN...VA..ARELVVNCCTE..HLISSEA.EICN.SEKKT.SPEH.
Retrocopy SSPDNTDDHAIPRAAISKTIKGALPNAQ<VASNARELVVNCCTELTHLISSEASEICNTSEKKTVSPEHT

Parental  IQALESLGFGSYISEVKEVLQECKTVALKRRKANSRLENLGIPEEELLRQQQELFAKARQQQAELAQQEW
          .QAL.SLGFG.YIS.VKEVLQ.CK.VAL.RRKA.S.LEN.GIPEE..L..QQEL..KA.QQQAELA.Q.W
Retrocopy LQALGSLGFGLYISAVKEVLQKCKMVALERRKASSHLENPGIPEEG*LSRQQELCTKAKQQQAELAPQDW

Parental  LQMQQ-AAQQAQLAAASAS
          L..Q...AQQA.LAAASAS
Retrocopy LPVQR<GAQQARLAAASAS

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	11.33 RPM
SRP017611_kidney	0.52 RPM	17.06 RPM
SRP017611_liver	0.00 RPM	9.36 RPM
SRP040447_lung	0.00 RPM	18.13 RPM
SRP040447_skeletal_muscle	0.00 RPM	10.27 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_518 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_518 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017815	1 retrocopy	retro_cjac_410,
Cavia porcellus	ENSCPOG00000003282	1 retrocopy	retro_cpor_518 ,
Loxodonta africana	ENSLAFG00000017540	1 retrocopy	retro_lafr_692,
Myotis lucifugus	ENSMLUG00000010684	1 retrocopy	retro_mluc_2349,