RetrogeneDB ID: retro_cpor_1136

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:28323282..28324624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CWC22
• Ensembl ID: ENSCPOG00000007492
• Aliases: None
• Description: None

Sequence

>retro_cpor_1136
AAAACAGAAGTTAATCTAGTCTCATTTCATCAAACAATATATCTTGCTATTCAATCCAGTCTAGATTTTGAAGAATGTGC
CCACAAATTGCTCAAAATGGAATTTCCTGCAAGTCAAACAAAAGAACTCTGCAGTATGATATCTGAATGCTGTGCCCAAC
AAAGAACATATGAGAAGTTTTTGGCATGTTAGCTGGGTGATTTTGCTTGCTGAGAAAAGAATACATGGGACCTTTTGAAA
GTGTATTCAAAGAACAGTATGATGCCATCCATCACCTAGAAACAAACAAATGGAGGAATGTTGCCAAGATGTTTGTTCAC
CTGTTTATACACTGATTTACTCCATGGAGTGTTCTTGAGTGTATAAAAATGAGTAAAGAAACTACTATATCATCTAGTAG
AATTTTTGTCAAAATACAATTTCAGGAACTGTTGAAATACATGGGTCTTCCTACACTAAACGCAACATTAAAGGACGATA
TCCGAAAGCCATTCTTTGAAGGAGGAGTGCCCTGTAACAACCCAAGAAACACTCAGTTTTCCACTATCTTCTTTACCGCT
ATAGGTCTTGGAGGTTCAATGAATGAACTGCATAAACATCTCAAAAATAAAAACAAAATTTACTGTGGCACAGAAAGCAA
ATGTTGAACCAAGTAAATCCTCTTCTTCCTCAGCACCTTCTTCGGAGTCTGACTCTACTGACTCTTATTCTGACAGCACT
GAGAGCAGTTCAAACTCTTCCAGTGAGGACGGCAACTCTTCATCCACCAGTAGCCACAGCTCTGCCTGGAATAAAGATAT
GAGAAAAAAGAGACAAGTGAAGTAAAGCTGGAGATAAGTCAGTCAGAAACCAACAAGTGACAGGAGACAGGAAGGAAGAA
GAGCAGAACAAAGGCACCAGGAAGCAAGGTCTGCGACAGAAAGGAGAACAGAAAAACACGGAAGTCAAAATTCAAGAGAT
TAGAATTATAGAGATCCCATAAGAAAACACACATCAGACAGGAGCGTCCTTTCCAAAGGAAACAGTTACCGTAGGGTCAG
TAATGACCGAGACCAAGAAACACATACGAGCTGGGAAAAGAAGCATGGTGATCCAGAAAAGAAGAGTGGAGACACAAGAA
AATTTCTTTGGAAAATGAGAATTACAGACTCTGAAATCAGGACAGTGAAAATTCTACAAGAACAGAGAGATCAAAGTCAG
AGAAAAGAACAGAAAATATGCAAGCTTGAAAAGTGAGGAAAATGGGTATCAGGATGGTGAGGAGAGACCGTGGGAAAAAT
CAAGCAGATACTCTGAGAGTTCCAGGGAGTCAAAGAAAACTCAGGACCAGAGAAGAGAGAAG

Alignment

ORF - retro_cpor_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 50.33 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KTEINLVSFRRTIYLAIQSSLDFEECAHKLLKMEFPESQTKELCNMILDCCAQQRTYEKF-FGLLAGRFC
          KTE.NLVSF..TIYLAIQSSLDFEECAHKLLKMEFP.SQTKELC.MI..CCAQQRTYEKF.FG.LAG.FC
Retrocopy KTEVNLVSFHQTIYLAIQSSLDFEECAHKLLKMEFPASQTKELCSMISECCAQQRTYEKF<FGMLAG*FC

Parental  MLKKEYMESFEGIFKEQYDTIHRLETNKLRNVAKMFAHL-LYTDSL-PWSVLECIKLSEETTTSSSRIFV
          .L.KEYM..FE..FKEQYD.IH.LETNK.RNVAKMF.HL.LYTD.L.PWSVLECIK.S.ETT.SSSRIFV
Retrocopy LLRKEYMGPFESVFKEQYDAIHHLETNKWRNVAKMFVHL>LYTDLL<PWSVLECIKMSKETTISSSRIFV

Parental  KIFFQELCEYMGLPKLNARLKDETLQPFFEGLLPRDNPRNTRFAINFFTSIGLGGLTDELREHLKNTPKI
          KI.FQEL..YMGLP.LNA.LKD....PFFEG..P..NPRNT.F...FFT.IGLGG...EL..HLKN..KI
Retrocopy KIQFQELLKYMGLPTLNATLKDDIRKPFFEGGVPCNNPRNTQFSTIFFTAIGLGGSMNELHKHLKNKNKI

Parental  -IVAQKPDVEQDGSSSSSASSSDSDSSDSGSDSSESSSDSSSGDSDSSSTSSHSSASGKDMRKKARGKTR
          ..VAQK..VE...SSSSSA.SS.SDS.DS.SDS.ESSS.SSS.D..SSSTSSHSSA..KDMRKK...K..
Retrocopy >TVAQKANVEPSKSSSSSAPSSESDSTDSYSDSTESSSNSSSEDGNSSSTSSHSSAWNKDMRKKRQVK*S

Parental  GKGGDKSVRSQQANDRRQEERRAEQRHQEARSERERRTEKHRSPNSRDQHWRDPMTKRASDRSGLSEGNS
          .........S......R..E....QRHQEARS..ERRTEKH.S.NSRD...RDP..K..SDRS.LS.GNS
Retrocopy WR*VSQKPTSDRRQEGRRAE----QRHQEARSATERRTEKHGSQNSRD*NYRDPIRKHTSDRSVLSKGNS

Parental  YSRVGNGRDPETRVDWEDKHGDPEKKRGERR-HIFLENENYRLRNQDSENSRRTERSKS-REKTRKHASS
          Y.RV.N.RD.ET...WE.KHGDPEKK.G..R..I.LENENYRL.NQDSENS.RTERSKS.REK.RK.AS.
Retrocopy YRRVSNDRDQETHTSWEKKHGDPEKKSGDTR<KISLENENYRL*NQDSENSTRTERSKS<REKNRKYASL

Parental  KSEEDRYQNGAERRWEKSSRYSEHSRESKKSQDRRRDK
          KSEE..YQ.G.ER.WEKSSRYSE.SRESKK.QD.RR.K
Retrocopy KSEENGYQDGEERPWEKSSRYSESSRESKKTQDQRREK

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	20.30 RPM
SRP017611_kidney	0.00 RPM	20.00 RPM
SRP017611_liver	0.00 RPM	11.71 RPM
SRP040447_lung	0.00 RPM	25.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	8.88 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1136 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1136 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007492	1 retrocopy	retro_cpor_1136 ,
Myotis lucifugus	ENSMLUG00000013437	1 retrocopy	retro_mluc_207,
Otolemur garnettii	ENSOGAG00000015287	1 retrocopy	retro_ogar_3200,