RetrogeneDB ID: retro_cpor_747

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:21224039..21224322(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL5B
• Ensembl ID: ENSCPOG00000005856
• Aliases: None
• Description: None

Sequence

>retro_cpor_747
ATTCTCTTCATCAGGATATGGAGACTGTTCAATTGCCAGTAAAACAAAGTTATCATTGCTGGTTTGAATAATGCAGGAAA
AAACTACTATCCTTTACCAGTTACCTGTGAATGAAGTTGTACATGTATCCCCTACAACAGGAAATAATGTAGAAAAGACA
GTGATTAATTATACATGTTTCTTGATGTGGAATATTGGTGGCCAAGAATTTCTTTGCTCTTTCTGGAACACTTACTATAT
TAATACAGAGTTTGTAATAGTTGTTGTGGACAGTATAGGGAGA

Alignment

ORF - retro_cpor_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.16 %
• Parental protein coverage: 52.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYFANLWSSFCYIEHKVIIVGLDNAG-KTTILYQFLMNEVVHTSPTIGSNVEEIVVKNTHFLMWDIGGQE
          ..F...W..F.....KVII.GL.NAG.KTTILYQ...NEVVH.SPT.G.NVE..V...T.FLMW.IGGQE
Retrocopy ILFIRIWRLFNCQ*NKVIIAGLNNAG>KTTILYQLPVNEVVHVSPTTGNNVEKTVINYTCFLMWNIGGQE

Parental  SLRSSWNTYYSNTEFIILVVDSIDR
          .L.S.WNTYY.NTEF.I.VVDSI.R
Retrocopy FLCSFWNTYYINTEFVIVVVDSIGR

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	2.53 RPM
SRP017611_kidney	0.00 RPM	1.67 RPM
SRP017611_liver	0.00 RPM	2.61 RPM
SRP040447_lung	0.00 RPM	0.88 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_747 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_747 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005209	1 retrocopy	retro_cpor_913,
Cavia porcellus	ENSCPOG00000005856	2 retrocopies	retro_cpor_558, retro_cpor_747 ,
Macaca mulatta	ENSMMUG00000007453	3 retrocopies	retro_mmul_614, retro_mmul_726, retro_mmul_743,
Oryctolagus cuniculus	ENSOCUG00000014876	1 retrocopy	retro_ocun_79,
Ictidomys tridecemlineatus	ENSSTOG00000027859	1 retrocopy	retro_itri_580,