RetrogeneDB ID: retro_cpor_93

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_45:9921649..9922096(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008201
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000023851
• Aliases: None
• Description: None

Sequence

>retro_cpor_93
ATGGAGCCAGAGGTCTTAGAAATTTGTCCTTACAACCCTCACCACCGAATTCCACTCAGCAGATTCCAGTACCACCTGGC
ATCGTGCAAGAGAAAAAACCCCACGAAAGCCAAGAAAATGGCCAGCTGCAAATACAATGCCTGCCACGTCGTCCCCATCA
AAAAGCTGGAGGAACACGAGGCTGCCTGTGCCAACAGAAGCCCCGTGGAGGAAGAGGGCAGCACAAACCCACTGGTGACG
CTTCTCAGTTCAGAGCAGAAAGCTGAAGCCCTGTGGGTCACCTCCTCCCCTCCCACCTCTGATATCTGGAATGCTGATGA
CGCTGATAGCCACCCTAAGTTTGTCCTTAAGACTTTTGTTCCCCAAAAGCTTGTTTGTGAAAGTGACGCAGGAGAGTCAG
AGAGAAAGGAGAACAACCTCCAGAAGATCTTCAGACCAGGAAAGTAA

Alignment

ORF - retro_cpor_93 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.18 %
• Parental protein coverage: 83.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEPEALKICPYIPTHKMPASRLQYHLVLCKKKNPNIAKKMANCKYNACHVVPIKRLKEHEANCVCRTAID
          MEPE.L.ICPY.P.H..P.SR.QYHL..CK.KNP..AKKMA.CKYNACHVVPIK.L.EHEA.C..R....
Retrocopy MEPEVLEICPYNPHHRIPLSRFQYHLASCKRKNPTKAKKMASCKYNACHVVPIKKLEEHEAACANRSPVE

Parental  DEPINLPLFISTSLELNEKLSNGASQIADPIVWNVGNMHHSSPFILKTFTPKLLVCE
          .E....PL....S.E.........S.......WN.........F.LKTF.P..LVCE
Retrocopy EEGSTNPLVTLLSSEQKAEALWVTSSPPTSDIWNADDADSHPKFVLKTFVPQKLVCE

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	0.00 RPM
SRP017611_kidney	0.73 RPM	0.00 RPM
SRP017611_liver	0.09 RPM	0.00 RPM
SRP040447_lung	0.18 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.05 RPM	0.01 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_93 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_93 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000029590	1 retrocopy	retro_acar_141,
Ailuropoda melanoleuca	ENSAMEG00000000958	1 retrocopy	retro_amel_91,
Cavia porcellus	ENSCPOG00000023851	1 retrocopy	retro_cpor_93 ,
Felis catus	ENSFCAG00000031316	1 retrocopy	retro_fcat_1,
Mustela putorius furo	ENSMPUG00000005664	1 retrocopy	retro_mputfur_116,
Mus musculus	ENSMUSG00000053508	1 retrocopy	retro_mmus_199,
Rattus norvegicus	ENSRNOG00000036830	1 retrocopy	retro_rnor_1938,