RetrogeneDB ID: retro_cpor_447

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:11128764..11129875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DTL
• Ensembl ID: ENSCPOG00000014965
• Aliases: None
• Description: None

Sequence

>retro_cpor_447
AGGCTTTGTAGCATAGAATCACAAACTAGTAGAAAAAAGTGCTTCAAAGAATGGATGGCTCACTGGAATGCTATCTTTGA
CTTGGCCTGGGTCCCAGGCAAGCTCAAACTTGTTACAGCAGCCAGTGATCAAACAGCCAAATTTTGGGACATAAAAGCTG
GTGAGTTGATTGGAACATGCAAGGTCATCAGTGCAGTCTCAAGTCAGTTGCGCTTTCTAAGTTTTAGAAAGTGTATCCTG
TACAGGTGGAAGAGACAGTAACATGATGGTCTGGGATACCAGTTGCAGTAAAAAAGATGGGTTCTAGGGGCAAGTGAACT
AAATCAATGGAACTTATAATCTGTCAGACAAGCAAACACCTTCAAAGTCCAAAAAGAAACAGAATTCTAAAGAACTTGTT
CCTTCTGTGAATTTCCAGAAGAGTGTTACTATAGCTGTTTTTCCAAGATGAGAATACAATAGTTTCAGGAGGAGCTGTGG
ATGGAATAATAAAAATATGGGATTTACACAAGAATTTTACTGCTTATTGACAAGAATCTTTAACATCTAAATCTTTCTTG
TGCCCAGGTAGCAGCACTCAAAAACTAGGATACTCCAGTTGATTTTGTATTCAACTGGCACCACTTTATTTGCTAATTGC
ACAGAGGACAACATCTATATGTTCAGTATTACTGGATTAAAGACCTCTCTGGTTGTTGTCTTCAGTGGACACCAGAACTC
TATCTTTTACTAAAATCAAGTCTTAGTCCAGATGACCAGTTTTTACTCAGTGGTTTGAGTAATGAAGCTGCCCACATATG
GAAGGTCTCTACACCCTCGCATCCACCTACCGTGCTCCTGGGTCACTCTTAAGAGGTCAGTTTTGTGTGCTAGTGTTCGT
CTGACTTCACCAAAATTGCTACCTGCTCTGCTGACAGCACATTAAAAATCTGGCACTTGAATAGAGGCTTAGAGGAGAAA
CCAGGAGCAGATATGAATTCCATAGTGGGTCTGTTCCTCTCAGAAGAAAAAAACAGACAAGATCAAGCCTGTAGGAGTAA
AAAGTACCCAGAAGACACCTGTCAAAGCCCCAAGGGCAAAGAGCAACCCAAGCCTGAGTACAGAGCTGAGC

Alignment

ORF - retro_cpor_447 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLYNTETQTIRKKCFKEWMAHWNAVFDLAWVPGELKLVTAAGDQTAKFWDVKAGELIGTCK-GHQCSLKS
          RL...E.QT.RKKCFKEWMAHWNA.FDLAWVPG.LKLVTAA.DQTAKFWD.KAGELIGTCK.GHQCSLKS
Retrocopy RLCSIESQTSRKKCFKEWMAHWNAIFDLAWVPGKLKLVTAASDQTAKFWDIKAGELIGTCK<GHQCSLKS

Parental  VAFSKFQK-AVFCTGGRDGNIMVWDTRCNKKDGFYRQVNQISGAHNTSDKQTPSKPKKKQNSKGLAPSVD
          VA.SKF.K..V.CTGGRD.N.MVWDT.C.KKDGF..QVN.I.G..N.SDKQTPSK.KKKQNSK.L.PSV.
Retrocopy VALSKF*K<SVSCTGGRDSNMMVWDTSCSKKDGF*GQVN*INGTYNLSDKQTPSKSKKKQNSKELVPSVN

Parental  FQQSVTVVLF-QDENTLVSAGAVDGIIKIWDLRKNYTAYRQEPIASKFFLYPGSSTRKLGYSS-LILDST
          FQ.SVT...F.QDENT.VS.GAVDGIIKIWDL.KN.TAY.QE...SK.FL.PGSST.KLGYSS.LIL.ST
Retrocopy FQKSVTIAVF>QDENTIVSGGAVDGIIKIWDLHKNFTAY*QESLTSKSFLCPGSSTQKLGYSS<LILYST

Parental  GSTLFANCTDDNIYMFNMTGLKTSPVAVFNGHQNSTFY-VKSSLSPDDQFLLSGSSDEAAYIWKVSTPWH
          G.TLFANCT.DNIYMF..TGLKTS.V.VF.GHQNS.FY..KSSLSPDDQFLLSG.S.EAA.IWKVSTP.H
Retrocopy GTTLFANCTEDNIYMFSITGLKTSLVVVFSGHQNSIFY<LKSSLSPDDQFLLSGLSNEAAHIWKVSTPSH

Parental  PPTVLLGHSQEVTSVCWCPSDFTKIATCSDDNTLKIWRLNRGLEEKPGADKHSIVG-WASQKKKEARSGL
          PPTVLLGHS.EV..VC.C.SDFTKIATCS.D.TLKIW.LNRGLEEKPGAD..SIVG...SQKKK......
Retrocopy PPTVLLGHS*EVSFVC*CSSDFTKIATCSADSTLKIWHLNRGLEEKPGADMNSIVG>CSSQKKKTDKIKP

Parental  VAVPSTQSTPAKAPRVKSSPVLSSPSS
          V.V.STQ.TP.KAPR.KS.P.LS...S
Retrocopy VGVKSTQKTPVKAPRAKSNPSLSTELS

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	0.46 RPM
SRP017611_kidney	0.00 RPM	1.47 RPM
SRP017611_liver	0.00 RPM	2.52 RPM
SRP040447_lung	0.00 RPM	5.20 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.61 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_447 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_447 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	ENSCPOG00000014965	1 retrocopy	retro_cpor_447 ,