RetrogeneDB ID: retro_cpor_558

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_190:340660..341191(+)
• 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_558
ATTCTCTTCACCAGGATATGGAGACTGTTCAATCACCAGGAACACAAAGTTATCATTGTTGGGTTGGACAATGCAGGGAA
AACTACCATCCTTTACCAGTTCTCCATGAATGAAGTTGTGCATACATCTCCTACAATAGGAAGTAATGTAGAACAGATAG
TGGTTAATAATACGTGTTTCCTGATGTGAGATATTGGTGGCCAAGAATCTCTTCGCTCTTCCTGGAACACTTACTATACT
AATACAGAGTTTGTAATAGTTGTTGTGGACAGTACAGACAGAGAGAGGATTTCTGTAACTAGAGAAGAACTCTACAAAAT
GTTAGCTCATGAGGACCTAAGGAAAGCTGGACTGCTGATTTTTGCTAATAAACAAGATGTTAAAGAATGCATGACTCTAG
CAGAAATCTCCCAGTTCTTGAAGCTCACTTCTATTAAAGATCATCAGTGGCATATCCAGGCATGCTGTGCTCTTACTGGT
GAAGGATTATGCCAAGGGCTTGAATGGATGATGTCACGACTTAAAATTAGA

Alignment

ORF - retro_cpor_558 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 98.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LYFANLWSSFCYIEHKVIIVGLDNAGKTTILYQFLMNEVVHTSPTIGSNVEEIVVKNTHFLMWDIGGQES
          ..F...W..F...EHKVIIVGLDNAGKTTILYQF.MNEVVHTSPTIGSNVE.IVV.NT.FLM.DIGGQES
Retrocopy ILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEQIVVNNTCFLM*DIGGQES

Parental  LRSSWNTYYSNTEFIILVVDSIDRERLAITKEELYRMLAHEDLRKAAVLIFANKQDMKGCMTAAEISKYL
          LRSSWNTYY.NTEF.I.VVDS.DRER...T.EELY.MLAHEDLRKA..LIFANKQD.K.CMT.AEIS..L
Retrocopy LRSSWNTYYTNTEFVIVVVDSTDRERISVTREELYKMLAHEDLRKAGLLIFANKQDVKECMTLAEISQFL

Parental  TLSSIKDHPWHIQSCCALTGEGLCQGLEWMTSRIGVR
          .L.SIKDH.WHIQ.CCALTGEGLCQGLEWM.SR...R
Retrocopy KLTSIKDHQWHIQACCALTGEGLCQGLEWMMSRLKIR

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	9.84 RPM	2.53 RPM
SRP017611_kidney	9.74 RPM	1.67 RPM
SRP017611_liver	6.31 RPM	2.61 RPM
SRP040447_lung	13.19 RPM	0.88 RPM
SRP040447_skeletal_muscle	6.29 RPM	1.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_558 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_558 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,