RetrogeneDB ID: retro_cpor_453

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:28118415..28119040(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HHLA2
• Ensembl ID: ENSCPOG00000021750
• Aliases: None
• Description: None

Sequence

>retro_cpor_453
GCCTTCCTCACTCCTGTGATGAAGTATGAAAGTAGGAACATAAGCAGCTTCCTGATGTGCACTGTGCTCAGTGTTTATCC
TCGTGCACACATCACGTGGAAAATGAACTCTGCATCTGTCTGTGGAGGCAAAACAGAAGAAACAGGATATTGGGGCTCTT
TTTCTGTTAGCAGTATTCTGAATAGCACAGGGTCAAAATCATCTTATGAGTGGATCAATTGAAAATTCCTTGCTGAAGCA
AACGTGGACAAGGTGGTGGACACAGGAAGGTGGCTTTTGTAAAAGGCAAAGTGAGTACTTTTCATTCTCATGTTAAGGAA
TAAGAAACCTTTCTCTACCAAATGAAGACTTCACAGTCACTCAGTCCGGATTGAAAAGGGAAATTTCTTCCATTTTAGGT
TGCTGTCGGAGCTCCTCACAAATTTCAACAATCAGTGAACCCCGACTTTCTTGGAACAAATAGCTGACAAACCAGAATGA
CTTCTCTATGACTTTGGCAGATCTTAGTCTTTCAGACAGTGGGGAATATTTGTGCAATATTTCTTCAGGAGGATATAGTC
TGCTCACAGTCCATACACTGCACATAGAACCAAGTTAAGAAAGAGCTTCCTGGATAATACCTGTT

Alignment

ORF - retro_cpor_453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.12 %
• Parental protein coverage: 50.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFLNPVMQYENRSTSSLLTCSVLSVYPRPHITWKMDSASISGSKTEETGYLGPFYVNSTLDITGSNSSYE
          AFL.PVM.YE.R..SS.L.C.VLSVYPR.HITWKM.SAS..G.KTEETGY.G.F.V.S.L..TGS.SSYE
Retrocopy AFLTPVMKYESRNISSFLMCTVLSVYPRAHITWKMNSASVCGGKTEETGYWGSFSVSSILNSTGSKSSYE

Parental  C-AIENPLLKQTWTGQWTQEGGLCKRQSEYLSLSCQGIRNFSLPNEDFTVTWSRLKSGTSSILGCYLSSS
          ...IEN.LLKQTWT..WTQEGG.CKRQSEY.S.SC.GIRN.SLPNEDFTVT.S.LK...SSILGC..SSS
Retrocopy W>SIENSLLKQTWTRWWTQEGGFCKRQSEYFSFSC*GIRNLSLPNEDFTVTQSGLKREISSILGCCRSSS

Parental  QTSKISEPRFSWNKELTNQSDFSMTLTDLSLSDSGEYLCNISSREYTLLTVHTLHIEPSQESISWIIPL
          Q.S.ISEPR.SWNK.LTNQ.DFSMTL.DLSLSDSGEYLCNISS..Y.LLTVHTLHIEPS.E..SWIIP.
Retrocopy QISTISEPRLSWNK*LTNQNDFSMTLADLSLSDSGEYLCNISSGGYSLLTVHTLHIEPS*ERASWIIPV

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	1.55 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.39 RPM
SRP040447_lung	0.00 RPM	0.00 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.00 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_453 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_453 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021750	1 retrocopy	retro_cpor_453 ,