RetrogeneDB ID: retro_cpor_603

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_2:30056462..30057002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: XPA
• Ensembl ID: ENSCPOG00000001544
• Aliases: None
• Description: None

Sequence

>retro_cpor_603
CATAAAGTTGGAAACATTGTTCCTCCACAAGTACAGTTATGGAATTGGGTTATACAATACGTGAAGAATGTAGTAAAGAA
TTTATGCATTTCTATGTTATGAATCACTTTGATGTGGCAACTTATAATAACTGCAGAGATTCTGATGAAAAATATAAGCT
TATTATCAAAACAGAAACAAAGCAAGAATATCTTCTAAAAGATTACAATTTAGAAAAAAAGAGAACCAATTCTTGAATGA
ATTGTGAAGAATCCTTATCATTCACATTGAGGAGATATGAAATTCTTTTTAAACCTACAGACTGTGAAGAGGCCTCTTAA
AGTTTGGAGTAGTCAGGAAGCATTAGAAGAAGCAAAGGCAGTAAGACAAGAAAACAGAGAAAAAATGAAATAGAAGAATG
TTGTTAAAAAAGGAACAGAATTGTGGAGAGTGGTGTGAAACAGACAAACAACTGCTCATCAGCAGGAGTCTGGACTGGAA
GAAAACTCAGAAGAAATGTACCACAGGACTTGTGCTGTGTGAAGTCACAAGCTGACATAT

Alignment

ORF - retro_cpor_603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.36 %
• Parental protein coverage: 73.81 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HKVGNIV-HQPGPVMEFDYTICEECGKEFMDSYLMNHFDLATCDNCRDPDEKHKLITKTEAKQEYLLKDC
          HKVGNIV......VME..YTI.EEC.KEFM..Y.MNHFD.AT..NCRD.DEK.KLI.KTE.KQEYLLKD.
Retrocopy HKVGNIV<SSTSTVMELGYTIREECSKEFMHFYVMNHFDVATYNNCRDSDEKYKLIIKTETKQEYLLKDY

Parental  DLEK-REPALKFIVKKNPHHSQWGDMKLYLKLQIVKRSLEVWGSEEALEEAKEVRQENREKMKQKKFDKK
          .LEK.REP.L..IVK.NP.HS..GDMK..L.LQ.VKR.L.VW.S.EALEEAK.VRQENREKMK.K...KK
Retrocopy NLEK>REPILE*IVK-NPYHSH*GDMKFFLNLQTVKRPLKVWSSQEALEEAKAVRQENREKMK*KNVVKK

Parental  VKELRRAVRSSVWKRGTTAHQHEYGPEENLDDDMYRKTCTVCGHELTY
          ..EL.R.....V..R.TTAHQ.E.G.EEN....MY..TC.V..H.LTY
Retrocopy GTELWRV----V*NRQTTAHQQESGLEEN-SEEMYHRTCAV*SHKLTY

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	3.16 RPM
SRP017611_kidney	0.00 RPM	4.61 RPM
SRP017611_liver	0.00 RPM	4.57 RPM
SRP040447_lung	0.00 RPM	5.04 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_603 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_603 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001544	2 retrocopies	retro_cpor_295, retro_cpor_603 ,