RetrogeneDB ID: retro_cpor_329

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_128:3278413..3279531(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP3CC
• Ensembl ID: ENSCPOG00000001113
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:H0UVH2]

Sequence

>retro_cpor_329
CGTGGACAGTATAGAGTGTGTGTTGTTTTCATGGAGTTGAAAGAATATCCTAAAACATTGTTTCAGCTTTGAGGAAATCA
TGAACGCAGGCATCTTACTGAATACTTCACCTTCAAATATGAATGTCTAGTCAAATATTCGGAATGGGTGTATGAGGCAT
GTATGGACATATTCGCTATCTTTTCCTTACTGCCCTCTTAACCCAGCAGCTTCTCTGTGTCCATGGAGAAATGTCACCAG
AAATCACTTGTTTAGATGATATTAGGAAATTAGACAGGTTTACTGAACCTCCGGCCTTTGGGGCAGCGGGTGACCTGCTT
TGGTCTGATCCCTTGGAGCATTCCGGCAGTGCAAAGACCATGGGAAACTATGCCCACGGTACTGTCCGAGGGGGCTCTTA
CTTTTTCAGTTGCCCTGCAGTTTGTGAGTCTTTACAGAACAATTTATCATCAAAAATCAGAGCCCATGAAGCTCAAGACG
CTGGGCATCAAATGTACAGGAAGAGCGAGACCACCGGCTTTCCATCACTTATTACAATTTTCTCTGCCCCTAATTACCTA
GATGTCTATAACAATAAAGCTGCAGTGTTGAAAACTGACACCGATGTCATAAATATCAGGCAGTTTAACTGTTCTCCACA
CTCCTGTTGGCTTCCAAACTTTATGCATGTTTTCACCTGGTCTTTGCCTTTTGTTGGGGAAAAAGTCACAGAGATGCTGG
TTAACATTCTGAATATATTCTCTGATAATAAACTGATGTCTGACAATGAAACAGAAGGAGGCACTGTGGTTCGAAAAGAG
ATGATCAAGAATAAAATCAGAGCCGGTGGGAAGACGGCCTGGGTCTTTTCGGTTCTTCACGAAGAGAGTGAGAGTGTGCT
GACCGTCAAGGGCCTCACACCCACAGGCACACTCCCCCAGAGCATCCCGTTGGGAGGAAAGCAGACGGTTGAGACTGCCA
CAGGAGAAGCAGTAGAGGCCCAGGAAGCCACCCAACAGTTTTCACTGCAGCACAAAATTCGGAGTTTTGGAAAAGCCTGA
GGACTGGATCGAATTAATGAGTGAATGGCACCTCAAAAAGACAGTGGACATGATGGGCCAGTGAAACTGGTGTGACCC

Alignment

ORF - retro_cpor_329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.57 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RGYFSIECVLFLWSLKIIHPKTLFLLRGNHECRHLTEYFTFKQECNLIKYSERVYEACMDTFDC-LPLAA
          RG.....CV.F...LK...PKTLF.L.GNHE.RHLTEYFTFK.EC.L.KYSE.VYEACMD.F...L.L.A
Retrocopy RGQYRV-CVVFM-ELKE-YPKTLFQL*GNHERRHLTEYFTFKYEC-LVKYSEWVYEACMDIFAI<LFLTA

Parental  LLNQQFLCVHGGMSPEITCLDDIRKLDRFTEPPAFGPVCDLLWSDPSEDYGSEKTLENYTHNTVRGCSYF
          LL.QQ.LCVHG.MSPEITCLDDIRKLDRFTEPPAFG...DLLWSDP.E..GS.KT..NY.H.TVRG.SYF
Retrocopy LLTQQLLCVHGEMSPEITCLDDIRKLDRFTEPPAFGAAGDLLWSDPLEHSGSAKTMGNYAHGTVRGGSYF

Parental  FSYPAVCEFLQNNNLLSIIRAHEAQDAGYRMYRKSQTTGFPSLITIFSAPNYLDVYNNKAAVLKYENNVM
          FS.PAVCE.LQNN.L.S.IRAHEAQDAG..MYRKS.TTGFPSLITIFSAPNYLDVYNNKAAVLK....V.
Retrocopy FSCPAVCESLQNN-LSSKIRAHEAQDAGHQMYRKSETTGFPSLITIFSAPNYLDVYNNKAAVLKTDTDVI

Parental  NIRQFNCSPHPYWLPNFMDVFTWSLPFVGEKVTEMLVNILNICSDDELMSDDETEGGTTVRKEIIKNKIR
          NIRQFNCSPH..WLPNFM.VFTWSLPFVGEKVTEMLVNILNI.SD..LMSD.ETEGGT.VRKE.IKNKIR
Retrocopy NIRQFNCSPHSCWLPNFMHVFTWSLPFVGEKVTEMLVNILNIFSDNKLMSDNETEGGTVVRKEMIKNKIR

Parental  AIGKMARVFSVLREESESVLTLKGLTPTGTLPLGVLSGGKQTIETATVEAVEAQEAIRGFSLQHKIRSFE
          A.GK.A.VFSVL.EESESVLT.KGLTPTGTLP.....GGKQT.ETAT.EAVEAQEA...FSLQHKIRSF.
Retrocopy AGGKTAWVFSVLHEESESVLTVKGLTPTGTLPQSIPLGGKQTVETATGEAVEAQEATQQFSLQHKIRSFG

Parental  EARGLDRINERMPPRKDSGHDGPAKLVTP
          .A.GLDRINE.M.P.KDSGHDGP.KLV.P
Retrocopy KA*GLDRINE*MAPQKDSGHDGPVKLV*P

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	14.90 RPM
SRP017611_kidney	0.10 RPM	11.31 RPM
SRP017611_liver	0.04 RPM	4.18 RPM
SRP040447_lung	0.00 RPM	14.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	34.95 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_329 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_329 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001113	1 retrocopy	retro_cpor_329 ,