RetrogeneDB ID: retro_cpor_1291

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_65:8175759..8177113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CEP70
• Ensembl ID: ENSCPOG00000008134
• Aliases: None
• Description: None

Sequence

>retro_cpor_1291
ATCTCTGCCAGCAACAATAAAATGAAAAATCTTCAAAAGGAGAATAGAGTTTTACAGTCAAAATGCCAGAATTACAAGAA
AAAAGAAATAGAACAGCAAATAATGCTTCTTTGCAAAACTATGTCTGTCAACTAAGAAAAGAGGAGAAAGAACAAATTCT
CACTCAAAACATGTTTTCTTACCTGTGCAAAGGAGTTCTTCACATAGTCATGGATTGACAGTTGCTTTGCTTGATTAATT
ATTAAGAATCTAAAATTAGAAAAATCCATGCACCTCTGTGTATAAAAAAGATGAAAGTCAATCAGAAGAATAAAATGATT
ATAAAAATATGACTGCTTCACCACCTCACCAAAGCCTTCTAATGTCATTGCCAAATCAACTCAAGAAGTCGAATTCCAAG
ATTAATGCACTTTTAGTGCATAGCTAAACCTTCCAAAAGATTTAGAAAGCAGGACCTTACAACATGAATAATACTTTATA
AGTGACAAGTGAAGAAACTGGAAAAATTCCTTAATAAAGAATAAAATTACAAGAGCTTATGAGTCATAAAAAACACTGAG
GACACAGAGAAAAAAGTGAACCCAGCAGAGAAAACCATCAACAGGCACTAGTTAAGCAGAGATACTTTCAGGTTCTGTGT
AGCATCAGCTCAACTATTTATAATCTGAGAGCTCCTTGATCATTTATAAACAGAGCAAAGGATCCCAACATTTAACAAAG
ACCTTGTTTAAGACTGTGGATTTGAACATCTTGTTCCTCTAATAGAAATGTGGGCAGGCAAACAGATATCCCTGAAGGAT
TTACATAATTCTGTAAGAATACTATATACAGATCTGATGCCTTGGCATAATTTTAAGAAACAGGATGAAAATGAAGGTGT
CATAGTTGGAAATCTGTTGTTTATGGTGAATTCTATGTTAGAGGAAGTTGAAAATTAGGAAAAGGACAGCAGCATGCCAA
AATTTCAATCTTTGCCAGCTATTGTATCTTACTTTCACAAATTTTTGCTGTACCTTCTCTAAATGGAGTCCATCTTCAAA
TGAATGAAGTTTATAGTAGGCATTGAGAAATGAACAATGCTGTGAGGAACCTCCAAGAACACTTAGAATTAGATAGTTTA
TCTTCATGGTGTGTACTGGTGAGCACAGCTGAAAAACTGTGTAGGCTGATTAATGAGGATGTGACTGAGCAGGGTAAGAA
AGTACCAGGACCTGAAGACCTCAATAGTGTTGTTAACAGATTGGAATAACAGGAGGAATTTTCCCCAGCATTTCAGGTAT
TTATTAGTGATCTACTTGAAATCTTAGAAACTGATGACTAGGATAAAATAAACAATTTAAAAGTACTTTCATAC

Alignment

ORF - retro_cpor_1291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.53 %
• Parental protein coverage: 80.28 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  VCQQQNQMKDLQKEHRTLQSKCQHYKKKQLEQHQTI-ASLQKDICRLKKEEEERVITQNRVFAYLCKRVP
          .....N.MK.LQKE.R.LQSKCQ.Y.KK.....Q...ASLQ...C.L.KEE.E...TQN..F.YLCK.V.
Retrocopy ISASNNKMKNLQKENRVLQSKCQNY-KKKEIEQQIM<ASLQNYVCQLRKEEKEQILTQN-MFSYLCKGVL

Parental  HTVLDKQLLCLIDYYESKIRKIFTQ-RQYRKDESQSEEEKDYRNLNVSRPYKGLLMSLQNQLKESNSKID
          H.V.D.QLLCLI.Y.ESKIRKI......Y.KDESQSEE..DY.N...S.P...LLMSL.NQLK.SNSKI.
Retrocopy HIVMD*QLLCLINY*ESKIRKIHAP<SVYKKDESQSEE*NDYKNMTASPPHQSLLMSLPNQLKKSNSKIN

Parental  ALL-SEKLKLQKDLENRPTQHE-LRLYKQQVKKLEKALKKN-IKLQELISYTK-TEDTEKK-DEANKENQ
          ALL.S..L.L.KDLE.R..QHE...LYK.QVKKLEK.L.K..IKLQEL.S..K.TEDTEKK..E...EN.
Retrocopy ALL<SA*LNLPKDLESRTLQHE<IILYK*QVKKLEKFLNKE<IKLQELMSHKK>TEDTEKK<SEPSRENH

Parental  QQALIDQRYFQVLCSINSIIHNPRAP-VIIYKQSKESQH-FNKDFVQDYGFEHLVPIIEMWADELTSLKD
          QQAL..QRYFQVLCSI.S.I.N.RAP..IIYKQSK.SQH.FNKD.V.D.GFEHLVP.IEMWA....SLKD
Retrocopy QQALVKQRYFQVLCSISSTIYNLRAP<LIIYKQSKGSQH<FNKDLV*DCGFEHLVPLIEMWAGKQISLKD

Parental  LYKSLKILSTELVPWHNFKKQDVSEGVRVEDLLFMVDAMLEEAENKKKDSNTPNFQTLQAIVSHFQK-LF
          L..S..IL.T.L.PWHNFKKQD..EGV.V..LLFMV..MLEE.EN..KDS..P.FQ.L.AIVS.F.K..F
Retrocopy LHNSVRILYTDLMPWHNFKKQDENEGVIVGNLLFMVNSMLEEVEN*EKDSSMPKFQSLPAIVSYFHK<IF

Parental  DVPSLNGVYPRMNEVYSRLGEMNNAVRNLQELLELDSSSSLCVLVSTVGKLCRLINEDVNEQVKQVLGPE
          .VPSLNGV...MNEVYSR..EMNNAVRNLQE.LELDS.SS.CVLVST..KLCRLINEDV.EQ.K.V.GPE
Retrocopy AVPSLNGVHLQMNEVYSRH*EMNNAVRNLQEHLELDSLSSWCVLVSTAEKLCRLINEDVTEQGKKVPGPE

Parental  DLQSIISRLEEHEEFFPAFQAFANDLLEILEIDDLDAIVPAVKKLKVLSY
          DL.S...RLE..EEF.PAFQ.F..DLLEILE.DD.D.I......LKVLSY
Retrocopy DLNSVVNRLE*QEEFSPAFQVFISDLLEILETDD*DKI----NNLKVLSY

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	11.04 RPM
SRP017611_kidney	0.00 RPM	20.52 RPM
SRP017611_liver	0.04 RPM	10.05 RPM
SRP040447_lung	0.00 RPM	9.99 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.77 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1291 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1291 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	ENSCPOG00000008134	1 retrocopy	retro_cpor_1291 ,