RetrogeneDB ID: retro_cpor_216

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_10:18867998..18868355(-)
• Located in intron of: ENSCPOG00000007938

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSCPOG00000010096
• Aliases: None
• Description: None

Sequence

>retro_cpor_216
GGACACTGTGGCAGGTGCTGCCCAGATGGCTGTGGAGGGACCCCAGAGACCCTGTCTTTCTTGGACAACCTCAGGACCTG
CTATGTAGATACTTTGTTTGGTAGCTGGAGAGGCTGGGTACAAAGACACTAAGGAATTACAGAACTGTTTGAAGATAATC
AGGCATTGCTGGAGAATGAAAAGCTTTTAATCTGAGACTTGTCCCTTTACGGTTTCAACTCTGGATAAAGATGTGTCTGG
CACAATGCAGTTCAAGGAGTTTAAAGAATTGTGGGATATATGAATGGCTGGAAACAATATTTCATCTGTTTTGGTAGTGA
GAGCAGTGGAACAATGGATCCTCAAGAATTTCAGGAG

Alignment

ORF - retro_cpor_216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.4 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GAGGGYYPGGFGGAPG-GPAFPAQTQDPQYGYFA-AVAGQDGQIDADELQRCLTQ-SGIAGGYKPFNL-E
          G..G...P.G.GG.P...P.F..Q.QD....YF...VAG..G..D..ELQ.CL...SGIAG..K.FNL.E
Retrocopy GHCGRCCPDGCGGTPE<DPVFLGQPQDLLCRYFV<LVAGEAGYKDTKELQNCLKI>SGIAGE*KAFNL<E

Parental  TCRLMVSMLDKDMSGTMGFTEFKELWSV-LNGWKQHFTSFDSDRSGTVDPQELHK
          TC...VS.LDKD.SGTM.F.EFKELW....NGWKQ.F..F.S..SGT.DPQE...
Retrocopy TCPFTVSTLDKDVSGTMQFKEFKELWDI<MNGWKQYFICFGSESSGTMDPQEFQE

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	0.46 RPM	38.42 RPM
SRP017611_kidney	0.52 RPM	73.07 RPM
SRP017611_liver	0.17 RPM	45.62 RPM
SRP040447_lung	0.38 RPM	64.92 RPM
SRP040447_skeletal_muscle	0.03 RPM	16.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_216 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_216 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216 ,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,