RetrogeneDB ID: retro_cpor_473

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:32861919..32862392(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5C
• Ensembl ID: ENSCPOG00000011190
• Aliases: None
• Description: RAB5C, member RAS oncogene family [Source:HGNC Symbol;Acc:9785]

Sequence

>retro_cpor_473
CTTTCTCACACAGACTGCCTGCATGAGAAGAGAGTCAAATTTGATATCTGGGACACAGCAGGCCAGGAACAGTACCACAG
CCTGACATCCATGTGCTACTCTGGGGGATGCAGGTGGTCACTGTGGTCTACATGACCAATGTGGACACTTCTGCACAGGC
CAGGAACTGGGTGAAGGAGCTGCAGCAGTAGGCCAGCCCCAGCATTATCATCACTCTGGTGGGAAACAAGGACGATCTGG
CCAACAAGCAGGCTGTGCAGTTCCAGGATGCACAAGCACATGCTGAGGACAACAGCCTGCTGTTCATGGAGACGTGTGCC
AAGACTTTTATGAATGTGAAAGAGATCTTCAAGGCCTTTGCCAAGAAGCTGCTGAAGAACAAGCAACAGAACACAACAGG
CACACCAAGCAGGAACCCAGGTGCAGTCCCATAGGAGAGCAACCTGGCCATGGGCGGCCAGTGCTGCAGCAAC

Alignment

ORF - retro_cpor_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.64 %
• Parental protein coverage: 73.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRGA-QAAIVVYDITNTDTFLRAKNWVKELQRQASPNI
          L..T.CL....VKF.IWDTAGQE.YHSL..M.Y.G.......V...TN.DT...A.NWVKELQ..ASP.I
Retrocopy LSHTDCLHEKRVKFDIWDTAGQEQYHSLTSMCYSGG<MQVVTVVYMTNVDTSAQARNWVKELQQ*ASPSI

Parental  VIALAGNKADLASKRAVEFQDAQAYAEDNSLLFMETSAKTAMNVNEVFMAIAKKLPKNEPQNVAGAPGRN
          .I.L.GNK.DLA.K.AV.FQDAQA.AEDNSLLFMET.AKT.MNV.E.F.A.AKKL.KN..QN..G.P.RN
Retrocopy IITLVGNKDDLANKQAVQFQDAQAHAEDNSLLFMETCAKTFMNVKEIFKAFAKKLLKNKQQNTTGTPSRN

Parental  RGVDLQESSPASRGQCCSN
          .G....ES..A..GQCCSN
Retrocopy PGAVP*ESNLAMGGQCCSN

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	44.17 RPM
SRP017611_kidney	0.00 RPM	87.62 RPM
SRP017611_liver	0.00 RPM	44.62 RPM
SRP040447_lung	0.00 RPM	139.67 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_473 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_473 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473 ,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73,