RetrogeneDB ID: retro_cpor_1172

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_52:2873928..2874231(-)
• Located in intron of: ENSCPOG00000002608

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3BGRL
• Ensembl ID: ENSCPOG00000012267
• Aliases: None
• Description: SH3 domain-binding glutamic acid-rich-like protein [Source:UniProtKB/TrEMBL;Acc:H0VL18]

Sequence

>retro_cpor_1172
GTGGTGATTTGTGTACATACTGCATCTTCTTCTGGTTCTATGGCAGTTAAGAAGAAACAGCAAGATGTGCTTGGTTTCAT
AGAAGCCAACACCACAGGATTTGAAGGAAAAGATACTGTAGCCAATGAAGAGACTCAGAAGTGGATAGGAGAAAACTGCG
CCTGGAACAGTTGACCAGCCACAGGGTGTCCCTTACCACCTCAGGTTTTCAAGGAGAGCCAGTACCGTGGAGACTATGAT
GCTGCCTTTGAAGCCCAAGAAAATAACGCAGCCTGTGCCTTTTTAGGCAGGAAGGCACCACCT

Alignment

ORF - retro_cpor_1172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVIRVYIASSSGSTAIKKKQQDVLGFLEANKIGFEEKDIAANEENRKWMRENVPENSRPATGYPLPPQIF
          .VI.V..ASSSGS.A.KKKQQDVLGF.EAN..GFE.KD..ANEE..KW..EN...NS.PATG.PLPPQ.F
Retrocopy VVICVHTASSSGSMAVKKKQQDVLGFIEANTTGFEGKDTVANEETQKWIGENCAWNS*PATGCPLPPQVF

Parental  NESQYRGDYD-AFEARENNAVYAFLGLKAPP
          .ESQYRGDYD.AFEA.ENNA..AFLG.KAPP
Retrocopy KESQYRGDYDAAFEAQENNAACAFLGRKAPP

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	12.88 RPM
SRP017611_kidney	0.00 RPM	33.50 RPM
SRP017611_liver	0.00 RPM	10.19 RPM
SRP040447_lung	0.00 RPM	40.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.55 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1172 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1172 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
Choloepus hoffmanni	ENSCHOG00000004130	1 retrocopy	retro_chof_647,
Callithrix jacchus	ENSCJAG00000003568	2 retrocopies	retro_cjac_1102, retro_cjac_140,
Cavia porcellus	ENSCPOG00000012267	3 retrocopies	retro_cpor_1172 , retro_cpor_244, retro_cpor_844,
Equus caballus	ENSECAG00000012612	1 retrocopy	retro_ecab_648,
Ictidomys tridecemlineatus	ENSSTOG00000013216	1 retrocopy	retro_itri_1152,