RetrogeneDB ID: retro_cpor_56

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:41651960..41653388(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000004917
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000003412
• Aliases: None
• Description: None

Sequence

>retro_cpor_56
AGAAGACAGGAAAGCATGCCTCAGACTCCTCCCTTTTCAGCAATGTTTGACAGCAGTGGTTACAACCGGAACCTCTATCA
GTCTGCAGAGGACAGCTGTGGAGGATTGTATTACCATGACAACAACCTCCTCTCTGGTTCTCTGGAAGCGCTTATCCAGC
ACTTGGTACCTAACGTGGATTACTACCCAGATAGAACATACATATTTACCTTCCTGCTCAGTTCACGGTTATTTATGCAC
CCCTATGAACTAATGGGCAAAGTTTGCCACTTATGTGTGGAGCATCAGAGGCTAAGTGATCCTGATGGTGATAAGAACCA
GATGAGAAAAATTGCACCTAAAATTCTTCAACTCTTGACAGAATGGACGGAAACATTTCCTTATGACTTTCGAGATGAAA
GAATGATGAGAAACTTGAAAGATCTGGCTCACAGAATAACCAGTGGTGAGGAGACGTACCGGAAGAATGTCCAGCAGATG
ATGCAGTGTCTCATCCGCAAACTTGCTGCTCTCAGCCAGTATGAGGAAGTCTTGGCAAAGATCAGCTCCACATCCACAGA
TCGGCTCACGGTCCTCAAGACCAAGCCGCAGTCCATCCAGAGGGATATCATCACTGTCTGCAGTGATCCATACACACTGG
CCCAGCAGCTGACTCACGTAGAGCTGGAGCGGCTCAATTACATTGGACCTGAAGATTTTGTTCAGGCATTTGTGCAGAAG
GATCCTTTGGACAATGACAAGAATTGCTTCAGTGAGCGGAAGAAAACACGAAACTTAGAAGCCTATGTGGAATGGTTTAA
TCGCTTAAGCTACTTGGTGGCTACAGAAATCTGCATGCCTGTTAAGAAGAAACACCGAGCACGAATGATTGAGTACTTCA
TTGACGTGGCTCGGGAGTGTTTTAACATTGGCAACTTTAATTCCTTGATGGCGATCATCTCTGGAATGAATATGAGTCCA
GTCTCACGGCTAAAGAAGACTTGGGTCAAGGTGAAGACTGCGAAGTTTGACATTCTTGAGCATCAAATGGACCCTTCCAG
CAACTTCTATAATTATCGAACAGCTCTTCGTGGGGCAGCTCAAAGGTCTTTAACTGCTCATAGTAGCAGAGAGAAGATAG
TGATACCGTTCTTCAGTCTCTTAATCAAAGACATTTATTTCCTCAATGAGGGCTGTGCCAACCGCCTTCCAAATGGCCAC
GTCAATTTTGAGAAATTTTGGGAACTGGCCAAACAAGTGAGTGAATTTATGACATGGAAACAAGTGGAGTGCCCTTTTGA
GAGGGACCGGAAGATCCTGCAGTACCTGCTCACGGTGCCTGTCTTCAGCGAAGATGCTCTCTATTTGGCTTCGTATGAGA
GTGAAGGACCTGAGAATCACATAGAGAAAGACAGATGGAAGTCTTTAAGGTCGAGCCTCTTGGGCAGA

Alignment

ORF - retro_cpor_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.36 %
• Parental protein coverage: 99.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQTPPFSAMFDSSGYNRNLYQSAEDSCGGLYYHDNNLLSGSLEALIQHLVPNVDYYPDRTYIFTFLLSS
          MPQTPPFSAMFDSSGYNRNLYQSAEDSCGGLYYHDNNLLSGSLEALIQHLVPNVDYYPDRTYIFTFLLSS
Retrocopy MPQTPPFSAMFDSSGYNRNLYQSAEDSCGGLYYHDNNLLSGSLEALIQHLVPNVDYYPDRTYIFTFLLSS

Parental  RLFMHPYELMGKVCHLCVEHQRLSDPDGDKNQMRKIAPKILQLLTEWTETFPYDFRDERMMRNLKDLAHR
          RLFMHPYELMGKVCHLCVEHQRLSDPDGDKNQMRKIAPKILQLLTEWTETFPYDFRDERMMRNLKDLAHR
Retrocopy RLFMHPYELMGKVCHLCVEHQRLSDPDGDKNQMRKIAPKILQLLTEWTETFPYDFRDERMMRNLKDLAHR

Parental  ITSGEETYRKNVQQMMQCLIRKLAALSQYEEVLAKISSTSTDRLMVLKTKPQSIQRDIITVCSDPYTLAQ
          ITSGEETYRKNVQQMMQCLIRKLAALSQYEEVLAKISSTSTDRL.VLKTKPQSIQRDIITVCSDPYTLAQ
Retrocopy ITSGEETYRKNVQQMMQCLIRKLAALSQYEEVLAKISSTSTDRLTVLKTKPQSIQRDIITVCSDPYTLAQ

Parental  QLTHVELERLNYIGPEEFVQAFVQKDPLDNDKNCFSERKKTRNLEAYVEWFNRLSYLVATEICMPVKKKH
          QLTHVELERLNYIGPE.FVQAFVQKDPLDNDKNCFSERKKTRNLEAYVEWFNRLSYLVATEICMPVKKKH
Retrocopy QLTHVELERLNYIGPEDFVQAFVQKDPLDNDKNCFSERKKTRNLEAYVEWFNRLSYLVATEICMPVKKKH

Parental  RARMIEYFIDVARECFNIGNFNSLMAIISGMNMSPVSRLKKTWAKVKTAKFDILEHQMDPSSNFYNYRTA
          RARMIEYFIDVARECFNIGNFNSLMAIISGMNMSPVSRLKKTW.KVKTAKFDILEHQMDPSSNFYNYRTA
Retrocopy RARMIEYFIDVARECFNIGNFNSLMAIISGMNMSPVSRLKKTWVKVKTAKFDILEHQMDPSSNFYNYRTA

Parental  LRGAAQRSLTAHSSREKIVIPFFSLLIKDIYFLNEGCANRLPNGHVNFEKFWELAKQVSEFMTWKQVECP
          LRGAAQRSLTAHSSREKIVIPFFSLLIKDIYFLNEGCANRLPNGHVNFEKFWELAKQVSEFMTWKQVECP
Retrocopy LRGAAQRSLTAHSSREKIVIPFFSLLIKDIYFLNEGCANRLPNGHVNFEKFWELAKQVSEFMTWKQVECP

Parental  FERDRKILQYLLTVPVFSEDALYLASYESEGPENHIEKDRWKSLRSSLLGR
          FERDRKILQYLLTVPVFSEDALYLASYESEGPENHIEKDRWKSLRSSLLGR
Retrocopy FERDRKILQYLLTVPVFSEDALYLASYESEGPENHIEKDRWKSLRSSLLGR

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	0.23 RPM	19.61 RPM
SRP017611_kidney	0.21 RPM	13.19 RPM
SRP017611_liver	0.09 RPM	7.92 RPM
SRP040447_lung	0.05 RPM	19.50 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_56 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_56 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003412	1 retrocopy	retro_cpor_56 ,
Dasypus novemcinctus	ENSDNOG00000005271	1 retrocopy	retro_dnov_2615,