RetrogeneDB ID: retro_cpor_1267

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_61:1470804..1471199(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCAN1
• Ensembl ID: ENSCPOG00000010683
• Aliases: None
• Description: None

Sequence

>retro_cpor_1267
AGCACCGCCATCGCCTGCCAGCTGGACTTGTGCATGTTCGCGGATGGCCTGTGCTGGGTCAAATTTGAATCCGCCTCTAG
GACATATGCGAAGAATGTCACCTTTCGGTACTTTAAGAGCTTCAGCGTGTCCGCATAAACTGCAGCAATCCATATCTGCA
GCAGATGCCAGATTGCGGCTGCAAAGACTGAGTTTCCAGGGAAGGAAATAAAGTTCTATTTTGCCCAGAGCTTACTACAC
ACAGGAAGCTCACACCTGGCTCCACCCAACCCAGACAAGCAGTTTCTGATCTCTCCTCCCACTTCCCCGCCAATGGGTTG
CAAACAGAGGAAGATGCTACTCCAGTCATAAATCAGGATCTTTTATATACTCTCTCCAAGCTGGGGCCAGGAGAG

Alignment

ORF - retro_cpor_1267 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 67.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SSLIACVANSDIFSESETRAKFESLFRTYDKDITFQYFKSF-KRVRINFSNP-LSAADARLQLH-KTEFL
          S..IAC......F.......KFES..RTY.K..TF.YFKSF..RVRIN.SNP..SAADARL.L..KTEF.
Retrocopy STAIACQLDLCMFADGLCWVKFESASRTYAKNVTFRYFKSF<QRVRINCSNP<ISAADARLRLQ<KTEFP

Parental  GKEMKLYFAQTL-HIGSSHLAPPNPDKQFLISPPASPPVGWKQ-VEDATPVINYDLLYAISKLGPGE
          GKE.K.YFAQ.L.H.GSSHLAPPNPDKQFLISPP.SPP.G.KQ..EDATPVIN.DLLY..SKLGPGE
Retrocopy GKEIKFYFAQSLLHTGSSHLAPPNPDKQFLISPPTSPPMGCKQ<EEDATPVINQDLLYTLSKLGPGE

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	9.55 RPM
SRP017611_kidney	0.00 RPM	24.08 RPM
SRP017611_liver	0.00 RPM	6.53 RPM
SRP040447_lung	0.00 RPM	14.02 RPM
SRP040447_skeletal_muscle	0.00 RPM	50.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1267 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1267 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002838	2 retrocopies	retro_cjac_4016, retro_cjac_437,
Cavia porcellus	ENSCPOG00000010683	1 retrocopy	retro_cpor_1267 ,
Tarsius syrichta	ENSTSYG00000006972	1 retrocopy	retro_tsyr_1913,