RetrogeneDB ID: retro_cpor_162

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:73774606..73775291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRA2B
• Ensembl ID: ENSCPOG00000006313
• Aliases: None
• Description: None

Sequence

>retro_cpor_162
GAAGACTCCCGTTTTGCTTCCAGAAGTGGAAGTGTTCACAAATGGAGGAAATCTGCAAGGCATACCCTGTAAGGTCTCGC
TCCGAGGAAGATTCCAGGCATTCCAGATCAAAGTGCAGGTCCAGATGTGAATCTAGGTCTAGATTTAGAAGTTCTCGCAA
GCATTATACAAGGTCACAATCTTGATCTTGTGCTCGTTGATGTTCCAGGAGCAGACCTCATAGTTGAGATTATCACAGAC
ACCACAGCCACAGCCACTCTCCCATGTCCACTCCAATGCATCATGTTGGAAATCAGGTAAATCCTGACCCAAACTGTTGC
CTTGGAATGTTTAGGTTGAGCTCATCCACCACAGGAAGAGATTTAAGAGAAGGGTTCTCTAAATATGGCTCAATTGCCAA
CATGTCTACTGTATGTGACCAGCAATCTAGGTGTTCAAGAGGGTTTGCCTTTGTGGATTTTGAAAATGTAGATGATGCCA
AGGAAGCCGAAGAGCATGCCAATTGAATGGAACTTGATGGGCGTAGGATCAGAGTTGATTTCTCTATAACAAAAAGACCA
CATACCCCAACACCAGGAATTTACATGGGGAGACTGACCTATTGCAGTTATACCATCAGGATTGCTATGACAGAGGATAC
TACTGTAGCTACGATGATCAGGACTACTATAGCTGGTCCTATAGA

Alignment

ORF - retro_cpor_162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.71 %
• Parental protein coverage: 85.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KESRSASRSGSAHGSGKSARHT-PARSRSKEDSRRSRSKSRSRSESRSRSRRSSRRHYTRSRSRSRSHRR
          ..SR.ASRSGS.H...KSARHT.P.RSRS.EDSR.SRSK.RSR.ESRSR.R.SSR.HYTRS.S.S.....
Retrocopy EDSRFASRSGSVHKWRKSARHT<PVRSRSEEDSRHSRSKCRSRCESRSRFR-SSRKHYTRSQS*SCAR*C

Parental  SRSRSYSRDYRRRHSHSHSPMSTRRRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIV
          SRSR..S.DY.R.HSHSHSPMST...HVGN..NPDPNCCLG.F.LS..TT.RDLRE.FSKYG.IA..S.V
Retrocopy SRSRPHS*DYHRHHSHSHSPMSTPMHHVGNQVNPDPNCCLGMFRLSSSTTGRDLREGFSKYGSIANMSTV

Parental  YDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIRVDFSITKRPHTPTPGIYMGRPTYGSSRRR-
          .DQQSR.SRGFAFV.FENVDDAKEA.E.AN.MELDGRRIRVDFSITKRPHTPTPGIYMGR.TY.S...R.
Retrocopy CDQQSRCSRGFAFVDFENVDDAKEAEEHAN*MELDGRRIRVDFSITKRPHTPTPGIYMGRLTYCSYTIR<

Parental  DYYDRGYDRGYDDRDYYSRSYR
          D.YDRGY...YDD.DYYS.SYR
Retrocopy DCYDRGYYCSYDDQDYYSWSYR

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	28.30 RPM
SRP017611_kidney	0.00 RPM	41.77 RPM
SRP017611_liver	0.00 RPM	25.07 RPM
SRP040447_lung	0.00 RPM	59.98 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.97 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_162 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_162 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013345	2 retrocopies	retro_cfam_1971, retro_cfam_966,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Cavia porcellus	ENSCPOG00000006313	1 retrocopy	retro_cpor_162 ,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778,
Rattus norvegicus	ENSRNOG00000001783	4 retrocopies	retro_rnor_1130, retro_rnor_1915, retro_rnor_2156, retro_rnor_2807,
Tarsius syrichta	ENSTSYG00000000388	1 retrocopy	retro_tsyr_1632,