RetrogeneDB ID: retro_cpor_175

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:35582066..35582441(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF141
• Ensembl ID: ENSCPOG00000007808
• Aliases: None
• Description: None

Sequence

>retro_cpor_175
CAGCTTTATAAAGACATGACAAGTCAAGCAGCAGGAGTGTTAACTCAGAGAGCCACCTCTGAAGAACCTGAGGAAAACTC
ATCCTCTGTAATGTCTTGTCAGGCTAGCCTTTGGAAGAGAAGGGTGAAGCAGCTGACCAATAGGAAGAGTGTTTATCTGC
ATAGATGGATTAGCTGACCTCAACCAGCTTGTGCTCATAACTTTTGCCAGAAATATATTGATAAATGAAGTGATCAACAC
AGAAACTGCCCCATTTGTTGCCTACAGATGACTGGAACAAATGAATCTCAGGTAGTGTCAGATGTACCCACAGTAGATGA
CATGGCTAACTATATTCTTAACATGGCTGATGAGGCAGGCCAGCCCCACAGGCCA

Alignment

ORF - retro_cpor_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 54.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLYKDMTSQAAEVLAQSCTSEEPDENSSSVTSCQASLWMGRVKQLTDE-EECC-ICMDGRADLILPCAHN
          QLYKDMTSQAA.VL.Q..TSEEP.ENSSSV.SCQASLW..RVKQLT...EEC..IC.DG.ADL.......
Retrocopy QLYKDMTSQAAGVLTQRATSEEPEENSSSVMSCQASLWKRRVKQLTNR<EECL<ICIDGLADLNQLVLIT

Parental  FCQKCI-DKWSDRHRNCPICRLQMTGANESWVVSDAPTEDDMANYILNMADEAGQPHRP
          F......DK.SD.HRNCPIC.LQMTG.NES.VVSD.PT.DDMANYILNMADEAGQPHRP
Retrocopy FARNIL<DK*SDQHRNCPICCLQMTGTNESQVVSDVPTVDDMANYILNMADEAGQPHRP

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	19.33 RPM
SRP017611_kidney	0.00 RPM	18.53 RPM
SRP017611_liver	0.00 RPM	7.14 RPM
SRP040447_lung	0.00 RPM	18.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_175 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_175 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011014	1 retrocopy	retro_cjac_3999,
Cavia porcellus	ENSCPOG00000007808	2 retrocopies	retro_cpor_175 , retro_cpor_198,
Macropus eugenii	ENSMEUG00000014558	1 retrocopy	retro_meug_1251,
Mus musculus	ENSMUSG00000030788	1 retrocopy	retro_mmus_2996,
Oryctolagus cuniculus	ENSOCUG00000002807	1 retrocopy	retro_ocun_1507,
Otolemur garnettii	ENSOGAG00000001765	1 retrocopy	retro_ogar_1262,
Sarcophilus harrisii	ENSSHAG00000002101	2 retrocopies	retro_shar_148, retro_shar_694,
Ictidomys tridecemlineatus	ENSSTOG00000019740	1 retrocopy	retro_itri_1573,