RetrogeneDB ID: retro_cpor_933

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:3076115..3076515(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL10
• Ensembl ID: ENSCPOG00000001642
• Aliases: None
• Description: None

Sequence

>retro_cpor_933
GCAGGGAAGCCTCTACTCAAAGGCCACACCCCCACCTGGTTCTTATCTCTGTTTTGCTGCCCAACAAGAACATTGAGGGA
GATCTACTAGAGATCAGGACAACAAGAACATGCACTTCTATGAGAAGGAGTTTGTGAATGAGGTCGTATTCTTGGTGGAT
ATGACTGACCATCTCTGACGGTCACGAGTCCAACAGAAACTACACAAATTTCTAGGCAAAGACCTAAGCTGCCTGTCCTG
GTGTTGTCCACTAAGCAGGACATAAGGAAGGCCATGAGGGTGGTGGAATTGAGGCAGGAGCTGGGCCTGCAGCTGCCAAT
GGCTAGTAAGACATTTTCCTCTTGACAGTGAGGGCTACCCATATGAGACTTATTTTGAAGAACCTGGCACTGAAAACATT

Alignment

ORF - retro_cpor_933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.75 %
• Parental protein coverage: 56.56 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SGKTPLEGHVPTWGFN-SVRLPTKDFEVDLLEIG-GSQNLRFYWKEFVNEVDVLVFMVDSADRLRLPWAR
          .GK..L.GH.PTW....SV.LP.K..E.DLLEI.....N..FY.KEFVNEV...VF.VD..D.L......
Retrocopy AGKPLLKGHTPTWFLS<SVLLPNKNIEGDLLEIR<DNKNMHFYEKEFVNEV---VFLVDMTDHL*RSRVQ

Parental  QELHKLLDKD-PDLPVVVVANKQDLSEAMSVVELQQELGLQ-AIDNQREIFFLAASIA-PAGSGFEEPGT
          Q.LHK.L.KD.P.LPV.V...KQD...AM.VVEL.QELGLQ.A......IF.L......P....FEEPGT
Retrocopy QKLHKFLGKD<PKLPVLVLSTKQDIRKAMRVVELRQELGLQ<AANG**DIFLLTVRAT<PYETYFEEPGT

Parental  VHI
          ..I
Retrocopy ENI

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	3.57 RPM
SRP017611_kidney	0.00 RPM	1.15 RPM
SRP017611_liver	0.00 RPM	0.96 RPM
SRP040447_lung	0.00 RPM	2.72 RPM
SRP040447_skeletal_muscle	0.00 RPM	23.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_933 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_933 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001642	3 retrocopies	retro_cpor_136, retro_cpor_1479, retro_cpor_933 ,
Dasypus novemcinctus	ENSDNOG00000002678	1 retrocopy	retro_dnov_2004,
Oryctolagus cuniculus	ENSOCUG00000016961	1 retrocopy	retro_ocun_219,