RetrogeneDB ID: retro_cpor_1051

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_41:8444561..8444840(+)
• Located in intron of: ENSCPOG00000003418

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF185
• Ensembl ID: ENSCPOG00000006556
• Aliases: None
• Description: None

Sequence

>retro_cpor_1051
TCTACAGGAGAGGAAGCACTGGGCAGCAGAACCCCAGAGAGAAGACCAGAGCTCAAGAATAGAGGGGCATTTCTAAGATC
TGGATTTGGAGATGGTGGCTTCCAGATGTCTTCTGGAATTGGTGACGTTCCCCTTTAACATGCTTGCCACAGCAATTAAC
ATAAATGATAGGCAGCCTCCTCCAGCTGTCCCTGGGACACCCCAGTATGCAGATGAGCAGTTCCTGTCACGCCTCTTCCT
GTTGTGACCCTCCTGATCATGCTCTGGCTCCTGATTGCC

Alignment

ORF - retro_cpor_1051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.69 %
• Parental protein coverage: 50.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  STGQQDPREKTPPRPQGQRPEPENRGGFQGFGFGDGGFQMSFGIG-AFPFGIFATAFNINDGRPPPAVPG
          STG.......TP.R....RPE..NRG.F...GFGDGGFQMS.GIG..FPF...ATA.NIND..PPPAVPG
Retrocopy STGEEALGSRTPER----RPELKNRGAFLRSGFGDGGFQMSSGIG>TFPFNMLATAININDRQPPPAVPG

Parental  TPQYADEQFLSRLFLF-VALLIMFWLLIA
          TPQYADEQFLSRLFL..V.LLIM.WLLIA
Retrocopy TPQYADEQFLSRLFLL<VTLLIMLWLLIA

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	8.63 RPM
SRP017611_kidney	0.00 RPM	10.99 RPM
SRP017611_liver	0.04 RPM	9.62 RPM
SRP040447_lung	0.03 RPM	9.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.13 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1051 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1051 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002828	1 retrocopy	retro_btau_432,
Cavia porcellus	ENSCPOG00000006556	1 retrocopy	retro_cpor_1051 ,