RetrogeneDB ID: retro_cpor_160

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_0:66536878..66537193(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM242
• Ensembl ID: ENSCPOG00000022213
• Aliases: None
• Description: None

Sequence

>retro_cpor_160
TTAGAGTCTTCCTCTTCACTGGAAACTCGGGGATCCATGGGCAACCAGATTTTCCTAGTTAAAGATGGAATTTTCCTGGG
TTCTGTTGCTGAGCAGGGATGATAGTTGGAGTTGTTACATTATCACTGGCTAAAAAGAAAAGCCCTGAATGGTTCCATAA
AGGGAGTGTAGCACAGCTGCCTTACTGGAGAGTGGTCTTCTCTTGCCTTGTGAGCTCTGGGCTAGGGCTCACTTTATGCC
TGGTATGGAGTTGGTGCGATCAGCTTTGCAGTCTAGAGATCTTTAGGAGCTCACACTTACTACTTTTGGAGGAGC

Alignment

ORF - retro_cpor_160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.82 %
• Parental protein coverage: 75.89 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VESSSSLEARGSTDDRLFLIKGGIFLGSVAA-AGMIAGFVTTLSLAKKKSPEWFNKGSVA-TAALPESG-
          .ESSSSLE.RGS.....FL.K.GIFLGSVA..AGMI.G.V.TLSLAKKKSPEWF.KGSVA.TAAL.ESG.
Retrocopy LESSSSLETRGSMGNQIFLVKDGIFLGSVAE<AGMIVG-VVTLSLAKKKSPEWFHKGSVA<TAALLESG<

Parental  SSLALRALGWGSLCAWCGVGVISFAVWKALGVHTMKDFRS
          SSLAL.ALG.GSL.AW.GVG.ISFAV...LG.HT....RS
Retrocopy SSLAL*ALG*GSLYAWYGVGAISFAV*RSLGAHTYYFWRS

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	3.57 RPM
SRP017611_kidney	0.00 RPM	5.65 RPM
SRP017611_liver	0.00 RPM	4.22 RPM
SRP040447_lung	0.00 RPM	2.95 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.96 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_160 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_160 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009699	1 retrocopy	retro_amel_1551,
Cavia porcellus	ENSCPOG00000022213	1 retrocopy	retro_cpor_160 ,
Equus caballus	ENSECAG00000016335	1 retrocopy	retro_ecab_898,
Homo sapiens	ENSG00000215712	1 retrocopy	retro_hsap_1016,
Macaca mulatta	ENSMMUG00000011814	1 retrocopy	retro_mmul_812,
Nomascus leucogenys	ENSNLEG00000010676	1 retrocopy	retro_nleu_222,
Otolemur garnettii	ENSOGAG00000007646	1 retrocopy	retro_ogar_946,
Pongo abelii	ENSPPYG00000017271	1 retrocopy	retro_pabe_853,
Pan troglodytes	ENSPTRG00000018735	1 retrocopy	retro_ptro_747,