RetrogeneDB ID: retro_cpor_1217

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_58:3559467..3560139(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCHL3
• Ensembl ID: ENSCPOG00000012261
• Aliases: None
• Description: None

Sequence

>retro_cpor_1217
GAAGGTCAGTGCTGGTTGCCACTGGAGACCAACCCTGAGGTTACCAACCAGTTTCTCACACAATTAGGTCTCCATCCTAA
CTGGCAGTTTGTTGATGTATACGGGATGGATCCTAAACTATTCGGCATGGTACCAAGACCAGTACTTCTTTTCCCTACTA
TAGAAGAATATGAAGTATTCAGAACAGAAGAGGAGCAAAAGTAAAATCTCAGAGACAGGATGTTACATCATCTGTGTATT
TCATGAAGCAAACCATCGGCAATGCCTGTAGAACAGCTAGAGTGATCCATGCTACTGCAAACAATAAAGACAAAATGCAC
TTGAATCTGGATCAAGCTTGAAAAACTTCCTAGGGCAGTCTGTGTGAGTGAGCCCTGAAGAGCGGCCAGATACCTGGAGA
ACTATGACACTATTCCAGTTACTCAGGAGACCAGTGCCCATGAAGGTCAGACTGAGGCACCAAATACAGATGAAAAAGTA
GACCTTACTTTTATTGCATTAGTTCATGTAGATGGGCATCTCTGTGAATTAGATGGGCGGAAACCATTTCCGATTAACCA
TGGGGAAACTAGTGATGAGACTGTACTAGCAGATGCCAAAGAAGTTTGCAAAAAGTTTATGGAACATGGCCCTGATGAAT
TAAGATTCAATGCAATTGCTCTTTCTGCAGCT

Alignment

ORF - retro_cpor_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.31 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGQRWLPLEANPEVTNQFLKQLGLHPNWQFVDVYGMDPELLSMVPRPVCAVLLLFPITEKYEVFRTEEEE
          EGQ.WLPLE.NPEVTNQFL.QLGLHPNWQFVDVYGMDP.L..MVPRPV....LLFP..E.YEVFRTEEE.
Retrocopy EGQCWLPLETNPEVTNQFLTQLGLHPNWQFVDVYGMDPKLFGMVPRPV----LLFPTIEEYEVFRTEEEQ

Parental  K-IKSQGQDVTSSVYFMKQTISNACGTIGLIHAIANNKDKMHFVWIQP-LKKFLEESVSMSPGER-ARYL
          K..KSQ.QDVTSSVYFMKQTI.NAC.T...IHA.ANNKDKMH....Q..LK.FL..SV..SP.ER.ARYL
Retrocopy K<VKSQRQDVTSSVYFMKQTIGNACRTARVIHATANNKDKMHLNLDQA<LKNFLGQSV*VSPEER<ARYL

Parental  ENYDAIRVTHETSAHEGQTEAPNIDEKVDLHFIALVHVDGHLYELDGRKPFPINHGKTSDETLLEDAIEV
          ENYD.I.VT.ETSAHEGQTEAPN.DEKVDL.FIALVHVDGHL.ELDGRKPFPINHG.TSDET.L.DA.EV
Retrocopy ENYDTIPVTQETSAHEGQTEAPNTDEKVDLTFIALVHVDGHLCELDGRKPFPINHGETSDETVLADAKEV

Parental  CKKFMERDPDELRFNAIALSAA
          CKKFME..PDELRFNAIALSAA
Retrocopy CKKFMEHGPDELRFNAIALSAA

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	12.08 RPM
SRP017611_kidney	0.00 RPM	12.04 RPM
SRP017611_liver	0.00 RPM	11.27 RPM
SRP040447_lung	0.00 RPM	11.17 RPM
SRP040447_skeletal_muscle	0.01 RPM	8.14 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1217 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1217 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000012261	1 retrocopy	retro_cpor_1217 ,
Equus caballus	ENSECAG00000024190	1 retrocopy	retro_ecab_400,
Myotis lucifugus	ENSMLUG00000003442	1 retrocopy	retro_mluc_362,
Mus musculus	ENSMUSG00000022111	1 retrocopy	retro_mmus_177,
Oryctolagus cuniculus	ENSOCUG00000006789	1 retrocopy	retro_ocun_382,
Otolemur garnettii	ENSOGAG00000017114	1 retrocopy	retro_ogar_2285,
Rattus norvegicus	ENSRNOG00000009530	1 retrocopy	retro_rnor_2227,