RetrogeneDB ID: retro_cpor_1541

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:4492251..4492840(-)
• Located in intron of: ENSCPOG00000008720

Retrocopy information

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

Parental gene information

• Parental gene symbol: CABYR
• Ensembl ID: ENSCPOG00000008281
• Aliases: None
• Description: None

Sequence

>retro_cpor_1541
AATCCATCAAACATCACTGATTTTGCAGCAGCTTATTTTAAACAACTTATATTGTTTAGAGAAGGTAGTACTTCTCTGGA
TATATAAGATCTGGTTAAACAGTTCCTTCAGGTCAAAGTACAGAAATGGTCAGATGGAATGATACTGGAGAAGAAACCAG
AACATTTAAAAGAATCTGAAGGAACATCTGTGGTCTTCAAAATCCACCCAGATGGAAAAATGCACAAACATAGAGCAGGG
CAACATTTCAGGTCCACAGCTCATCAACAAAACCACCCAGTTTCCATTAGTTAGTGCCGAGGGCCTGCAGCCTGGAACAG
CTGAAGCAGTTCAAGGCTCTTCTTCCAAGCCAGCCACACCCAAGGCCACCACCCCCACCCCATCACCACCTGTAGCACCC
TACTCATCCTCAGCAGACCTTGCTCAGTTTACCACTCGGATGCTAGCAATAGCAACAAGTGAAGCAGAACCACCACCACC
ATATTCTAATAACATGTAGACTCCTTATTGTCTAACTAATACGAATCAACAAAGCTTCCTATCACTGCCACATGCACCTG
TGCCTTTCCTGCAAGTAACTATTTATCTA

Alignment

ORF - retro_cpor_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.99 %
• Parental protein coverage: 53.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NPSNITEFAAVYFKELIVFREGNTSLDIKDLVKQFHQIKVEKWSEGMTLSKKLERLKESEGTAEVF-QEP
          NPSNIT.FAA.YFK.LI.FREG.TSLDI.DLVKQF.Q.KV.KWS.GM.L.KK.E.LKESEGT..VF.Q.P
Retrocopy NPSNITDFAAAYFKQLILFREGSTSLDI*DLVKQFLQVKVQKWSDGMILEKKPEHLKESEGTSVVF<QNP

Parental  -TRMEKCTNTEEDNISGPQFINKTTQFPTESAECLQPEPAEAVPGNSPSSKPATPKAATPPTSPSPAPVS
          .T.MEKCTN.E..NISGPQ.INKTTQFP..SAE.LQP..AEAV.G.S..SKPATPKA....T.P.P.P..
Retrocopy <TQMEKCTNIEQGNISGPQLINKTTQFPLVSAEGLQPGTAEAVQGSS--SKPATPKA----TTPTPSPPV

Parental  AEFAYVPADPAQFATQMLAIATSEAGQSPPYSSNMWTLYCLTDMNQQSRPSPPPAPGPLPQATLYL
          A......AD.AQF.T.MLAIATSEA...PPYS.NM.T.YCLT..NQQS..S.P.AP.P..Q.T.YL
Retrocopy APYSS-SADLAQFTTRMLAIATSEAEPPPPYSNNM*TPYCLTNTNQQSFLSLPHAPVPFLQVTIYL

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	9.95 RPM
SRP017611_kidney	0.00 RPM	3.14 RPM
SRP017611_liver	0.00 RPM	24.24 RPM
SRP040447_lung	0.03 RPM	4.79 RPM
SRP040447_skeletal_muscle	0.01 RPM	8.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1541 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1541 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020641	1 retrocopy	retro_cjac_1459,
Cavia porcellus	ENSCPOG00000008281	1 retrocopy	retro_cpor_1541 ,
Loxodonta africana	ENSLAFG00000014928	1 retrocopy	retro_lafr_899,