RetrogeneDB ID: retro_cpor_1382

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_79:3090925..3091310(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TGIF2-C20orf24
• Ensembl ID: ENSCPOG00000011435
• Aliases: None
• Description: TGIF2-C20orf24 readthrough [Source:HGNC Symbol;Acc:44664]

Sequence

>retro_cpor_1382
ATGAGCAGTGGTGGGTAGAAGGAGGAGCCCTGTCAACCACAGCTGGCCATCAGGGCCCTCAAATCTCAGTTTGGAGCAAG
GTGCTGCAGAGTGATGTGGCCTGGGAGGACAAGGATGAATTTTAGATGTGATCTACTGGTTTCAACAGATCACTGCTGTG
GTCGTCAGTGTCATCTGGAGAGTTTATCCATTGCGAGGTTTCTTGGGAATTCCAGGATTCTGCTTGCTCAATGCAGAAGT
CCTATACCTTTACTTCAGTCAACTGCCTACAGATTGATGAGGAAGAATATGGCAGCACACAGGAATTCACAAAAGAAGAA
TTTATGACATCTTTTGTTTATTTGTGGTCATTTGGATCATTTTTTATACTGCCACCCACTATGAT

Alignment

ORF - retro_cpor_1382 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MSGGRRKEEPSQPQLANGA-PKVSVWSKVLRSDAAWEDKDEF-LDVIYWFRQIIAVVLGVIWGVLPLRGF
          MS.G..KEEP.QPQLA..A.P..SVWSKVL.SD.AWEDKDEF.LDVIYWF.QI.AVV..VIW.V.PLRGF
Retrocopy MSSGG*KEEPCQPQLAIRA<PQISVWSKVLQSDVAWEDKDEF<LDVIYWFQQITAVVVSVIWRVYPLRGF

Parental  LGIAGFCLINAGVLYLYFS-NYLQIDEEEYGGTWELTKEGFMTS-FALFMVIWIIFYTAIHYD
          LGI.GFCL.NA.VLYLYFS.N.LQIDEEEYG.T.E.TKE.FMTS.F.LF.VIWIIFYTA.HYD
Retrocopy LGIPGFCLLNAEVLYLYFS>NCLQIDEEEYGSTQEFTKEEFMTS<FCLFVVIWIIFYTATHYD

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	13.52 RPM
SRP017611_kidney	0.00 RPM	35.49 RPM
SRP017611_liver	0.00 RPM	51.41 RPM
SRP040447_lung	0.00 RPM	24.39 RPM
SRP040447_skeletal_muscle	0.00 RPM	13.64 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1382 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1382 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021805	1 retrocopy	retro_btau_697,
Cavia porcellus	ENSCPOG00000011435	2 retrocopies	retro_cpor_1090, retro_cpor_1382 ,
Mustela putorius furo	ENSMPUG00000017777	1 retrocopy	retro_mputfur_1460,
Otolemur garnettii	ENSOGAG00000000891	1 retrocopy	retro_ogar_1796,
Rattus norvegicus	ENSRNOG00000020317	1 retrocopy	retro_rnor_2185,