RetrogeneDB ID: retro_cpor_1112

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_47:10442858..10443332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TROAP
• Ensembl ID: ENSCPOG00000014679
• Aliases: None
• Description: None

Sequence

>retro_cpor_1112
ATCAGTTCTAAGAGATGCCTGCCTTTCCCTACAGTCAGACTGAGTGTCCAGGACCAGCAGTAACAAGACCCAAGAAGGCG
GTGCAGAAGCTGCCACTCAGGATTCAGTGTTCTGTCAACTCAACAGGCTCCAGGTGGAAAGTCATGCACCAAAAAGAGAT
ATCAAATGGTTAATGGGGATCACGCAGTTCCAAAACCCATCAGAGGAGCTCAGGCCTAGTACCAGGGGGCAAAACATGGG
GTTTGGTTGCCTCCCTAGAAAGAAGCTCTATAGTCCAGAGTTTGTAGCTGACCCTGCTGCCCTGGTCAGCATCCCGTCAG
GCGAGAGAGTGACGTGCTGCCAACAGGGTGCTGGTGCAGTCTGGCTCAGAGAGTGCTGGTTTGACAGAGCCTGGGCAGCG
CCATCTAGAGAGGCCAGGGTGCTCTGACCTCTGCATATATGGACCCCAGAACCCCCATCCATCAAGTGAGCCCA

Alignment

ORF - retro_cpor_1112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.22 %
• Parental protein coverage: 56.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VRSRRRPPFLTVKPSAQDQENQDPRT-LMEKSQLSIQRNFVDSAGPSSKATHQTEKSQR-SMAITQLRNP
          ..S.R..PF.TV..S.QDQ..QDPR.....K..L.IQ...V.S.G...K..HQ.E.S....M.ITQ..NP
Retrocopy ISSKRCLPFPTVRLSVQDQQ*QDPRR<AVQKLPLRIQCS-VNSTGSRWKVMHQKEISNG<LMGITQFQNP

Parental  LEELRPSPGEQNSGLGPPPQTEAPGPIEFVADPVALATILSGEGVKSC-PMGRQSSLAQRVLVRESQGGT
          .EELRPS...QN.G.G..P......P.EFVADP.AL..I.SGE.V..C.P.G...SLAQRVLV..S.G..
Retrocopy SEELRPSTRGQNMGFGCLPRKKLYSP-EFVADPAALVSIPSGERVTCC<PTGCWCSLAQRVLV*QSLGSA

Parental  IRRGQVSRASAYLAPRTPMHQLGP
          I.RGQ....SAY..PRTP.HQ..P
Retrocopy I*RGQGALTSAYMDPRTPIHQVSP

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	0.40 RPM
SRP017611_kidney	0.00 RPM	0.63 RPM
SRP017611_liver	0.00 RPM	0.44 RPM
SRP040447_lung	0.03 RPM	2.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1112 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1112 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014679	1 retrocopy	retro_cpor_1112 ,