RetrogeneDB ID: retro_cpor_811

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:6815229..6816014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UGP2
• Ensembl ID: ENSCPOG00000008459
• Aliases: None
• Description: None

Sequence

>retro_cpor_811
CAAAGCAGGTATCCATGGATTAGCAAAGAACATTTACTTCCTGTATCAAAGGATGTATCTTACTTGGCGGAAAAACAGAA
GCTTGGTGCCCTCTAGGTCATGGTAGCATCTATTCTATATCTGATTTGCTTGATGTCTTATAGGAGAAGGCAAAGAATAT
ATTTTTGTGTGTAACATAGATAATCTGGGTGCCACAGTGGATCTGTATATTCTTAATCTGATGAACACACCCAATGGAAA
ACCCTGTGAGTTTGTCATGGAAATCACAAATAAAATGTGAGCAGATGTAAAGTGTGAAACATTCATTCAGTGTGAAGGCA
AACTGAGAGTGGTAGAAATTACCCAAGTGCCAAAAGAACGTGTTGATAATTCCAATCTGTATCAATATTTAAAATATTTA
ACAGAAACAGCCTATGCATTTCTCTTGTAGCTGTTAAAAGACAGCAAGGATCAGAATGCCATTGCCATGGATACCGTTGT
GAATCCAAAGACTTTGGATGGAGGCCTTAAGTGTTATGTGGTTAGACACTGCAATGGGGACTGCAATTAAAAGTTTTGAG
ACTCCCTTAGGTATTAATGTTGCAGGAAGCCGTTTTTTTTTTCTATCAAAAATCACATCAGTTCTCTTGCTTGTGATTTT
AAACCTCTGTAGTCTTAATGCAGGATTTTTGAAGGTGCATCAAAAATGAGAATTTTGTGTCATGCCCTTGGTTAAATTAG
GTAGTTCACTTACCAAAGTTTAAAATTATCTAAGGATGTTTGAAAGTATACCAAATATGCTTGAA

Alignment

ORF - retro_cpor_811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.53 %
• Parental protein coverage: 52.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  QSRYPRINKESLLPVAKDVSYSGEN-TEAWYPPGHGDIYASFYNSGLLDTF-IAEGKEYIFVSNIDNLGA
          QSRYP.I.KE.LLPV.KDVSY..E..TEAW.P.GHG.IY.....S.LLD...I.EGKEYIFV.NIDNLGA
Retrocopy QSRYPWISKEHLLPVSKDVSYLAEK<TEAWCPLGHGSIYSI---SDLLDVL<IGEGKEYIFVCNIDNLGA

Parental  TVDLYILNHLMNPPNGKRCEFVMEVTNKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDE-FKSVSKFKI
          TVDLYILN.LMN.PNGK.CEFVME.TNK..ADVK..T..Q.EGKLR.VEI.QVPK..VD..F.SVS.FKI
Retrocopy TVDLYILN-LMNTPNGKPCEFVMEITNKM*ADVKCETFIQCEGKLRVVEITQVPKERVDN<FQSVSIFKI

Parental  FNTNNLWISLAAVKRLQ-EQNAIDMEIIVNPKTLDGGL-NVIQLETAVGAAIKSFENSLGINVPRSRFLP
          FN.N.L.ISL.AVKR.Q..QNAI.M...VNPKTLDGGL..V..L.TA.G.AIKSFE..LGINV..S....
Retrocopy FNRNSLCISLVAVKRQQ>DQNAIAMDTVVNPKTLDGGL>SVMWLDTAMGTAIKSFETPLGINVAGSXXXX

Parental  V-KTTSDLLLVMSNLYSLNAGSLTMSEKREFPTVPLVKLGSSFTKVQDYLRRFESIPDMLE
          ..K.TS.LLLV..NL.SLNAG.L....K.EF...PLVKLGSS.TKV..YLR.FESIP.MLE
Retrocopy LSKITSVLLLVILNLCSLNAGFLKVHQK*EFCVMPLVKLGSSLTKV*NYLRMFESIPNMLE

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	47.51 RPM
SRP017611_kidney	0.00 RPM	120.08 RPM
SRP017611_liver	0.00 RPM	265.77 RPM
SRP040447_lung	0.00 RPM	51.40 RPM
SRP040447_skeletal_muscle	0.00 RPM	150.91 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_811 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_811 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006960	1 retrocopy	retro_cjac_1709,
Cavia porcellus	ENSCPOG00000008459	1 retrocopy	retro_cpor_811 ,
Microcebus murinus	ENSMICG00000006509	1 retrocopy	retro_mmur_1277,
Oryctolagus cuniculus	ENSOCUG00000002137	1 retrocopy	retro_ocun_815,
Tursiops truncatus	ENSTTRG00000000694	1 retrocopy	retro_ttru_56,