RetrogeneDB ID: retro_cpor_53

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_92:2011966..2013946(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000020978
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDX3X
• Ensembl ID: ENSCPOG00000013557
• Aliases: None
• Description: None

Sequence

>retro_cpor_53
ATGAGTCGTACGACGGTGGGAAACGCGCTGGGCGGTGTAGACCAGCAGTTTTCTGGTCTCGACCTGAACGCTTCTGGTCA
TCAGAGTGGGGGAGCGAGTGGAGCCAGCAAAGGACGTTACATCCCTCCTCACCTCAGGAACAGAGACGCATCCAAAGGAC
TCTCGGATAGGGAAAGCTCAGCATGGAGCTGCGGTAGAGACAAGGATGCCTACAGCAGTTTTGGGTCTCGTGATTCGCGG
GGCAAGTCCAGTTACGTCAGTGATCGTGGAAGTGGAGCGAGGGGAAGATTTGATGACCGTGGGCGGAGCGGCTGTGACAG
CGCGGGCAGCCGCGACAGAGCTGGCTTTGGCAAATTTCAACGGAGTGAACATAGTCGCTGGTGTGAGCGATCGGATGAAG
ACGATTGGTCAAAACCACTTCCACCCAGTGAACGCTTAGAACAGGAGCTCTTCTCAGGAGGAAATACCGGGATTAACTTT
GAGAAGTACGACGATATACCAGTAGAGGCAACTGGCAACAACTGCCCTCCACACATTGAAAATTTCAGTGATGTCGACAT
GGGTGAAATTATCATGGGGAACATTGAGCTCGCTCGTTATACTCGTCCGACTCCAGTGCAAAAACACGCAATTCCTATTA
TCAAAGAAAAAAGAGACTTAATGGCTTGTGCTCAAACAGGGTCTGGGAAAACGGCAGCGTTTCTTCTACCCATCCTGAGT
CAGATATATACGGATGGTCCAGGAGAGGCTTTAAAGGCTGCAAAAGAAAACGGAAGGTATGAGCGCCGCAAGCAGTACCC
ACTCTCCTTGGTGTTGGCCCCAACGAGAGAACTGGCAGTACAGATCTACGAGGAAGCCAGAAAATTTTCATACCGGTCTA
GAGTTCGCCCTTGTGTAGTTTATGGCGGTGCTTGCATTGGCCAGCAGATCCGAGACTTAGAACGCGGATGTCACCTACTC
GTTGCCACTCCAGGACGTTTGGTGGATATGATGGAAAGAGGAAAAATTGGATTAGACTTCTGCAAATACTTAGTATTAGA
TGAAGCTGACAGGATGCTGGATATGGGATTTGAACCTCAGATACGGCGCATAGTAGAACAAGATACTATGCCACCAAAGG
GTGTCCGTCACACTATGATGTTTAGTGCTACCTTTCCTAAGGAGATACAGATGCTTGCTTGTGACTTCTTGGATGAATAT
ATCTTTCTGGCTGTAGGCAGAGTAGGCTCTACTTCTGAGAACATCACCCAGAAAGTAGTTTGGGTGGATGAGATGGACAA
ACGGTCATTTCTGCTTGATCTCTTGTGTGCAACAGGAAAAGACTCACTGACTTTAGTGTTTGTGGAGACCAAAAAGGGTG
CAGATTCTCTGGAGGATTTCTTATATCATGAAGGTTTTGCCTGTGCCAGCATTCATGGAGACAGATCGCAGAGAGATCGA
GAGGAAGCACTTCGCCAGTTCCGCTTGGGGAAAAGTCCAATTCTGGTTGCTACAGCTGTGGCAGCCAGAGGTCTAGACAT
TTCAAACGTGAAACACGTTATCAACTTTGATTTGCCAAGTGACATTGAGGAATATGTGCATCGCATTGGTCGTACAGGGC
GTGTAGGAAACCTTGGCCTTGCCACCTCCTTCTTCAATGAAAGAAATGCAAACATCACAAAGGATTTGTTGGATCTTCTT
ATAGAAGCTAAACAAGAGGTCCCATCTTGGTTGAAAAATATGGCTTTTGAACATCATCACAAGGGGAGCAGTCGTGGACG
TTCTAAGAGCAGATTCACTGGAGGATTTGGTGGCAGAGACTACCGACAAAATAGTGGTTCTGGCAGTTCTTGCAACAATC
GTGCCAGCAGTAGCCGCAGTGGTGGAGGTAGTCATGGTAATAGCAGAGGATTTGGTGGAGGTGGCTATGGAGGCTTCTAC
AGTAGTGATGGGTATGGTGGGAATTATAACTCCCAGAGTGTTGACTGGTGGGGCAACTGA

Alignment

ORF - retro_cpor_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 99.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NALG-LDQQFAGLDLNSSDNQTGGST-ASKGRYIPPHLRNREATKGYYDKDSSGWSSSKDKDAYSSFGSR
          NALG..DQQF.GLDLN.S..Q.GG...ASKGRYIPPHLRNR.A.KG..D..SS.WS...DKDAYSSFGSR
Retrocopy NALGGVDQQFSGLDLNASGHQSGGASGASKGRYIPPHLRNRDASKGLSDRESSAWSCGRDKDAYSSFGSR

Parental  NDSRGKSSFFSDRGSGSRGRFDDRGRGDYDGIGSRGDRGGFGKFERGGNSRWCDKSDEDDWSKPLPPSER
          .DSRGKSS..SDRGSG.RGRFDDRGR...D..GSR.DR.GFGKF.R...SRWC..SDEDDWSKPLPPSER
Retrocopy -DSRGKSSYVSDRGSGARGRFDDRGRSGCDSAGSR-DRAGFGKFQRSEHSRWCERSDEDDWSKPLPPSER

Parental  LEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIK
          LEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIE.FSDV.MGEIIMGNIEL.RYTRPTPVQKHAIPIIK
Retrocopy LEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIENFSDVDMGEIIMGNIELARYTRPTPVQKHAIPIIK

Parental  EKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEE
          EKRDLMACAQTGSGKTAAFLLPILSQIY.DGPGEAL.A.KENGRY.RRKQYP.SLVLAPTRELAVQIYEE
Retrocopy EKRDLMACAQTGSGKTAAFLLPILSQIYTDGPGEALKAAKENGRYERRKQYPLSLVLAPTRELAVQIYEE

Parental  ARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM
          ARKFSYRSRVRPCVVYGGA.IGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM
Retrocopy ARKFSYRSRVRPCVVYGGACIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDM

Parental  GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRVGSTSENITQKVVWVEEL
          GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLA.DFLDEYIFLAVGRVGSTSENITQKVVWV.E.
Retrocopy GFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLACDFLDEYIFLAVGRVGSTSENITQKVVWVDEM

Parental  DKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDREEALHQFRSGKSPIL
          DKRSFLLDLL.ATGKDSLTLVFVETKKGADSLEDFLYHEG.AC.SIHGDRSQRDREEAL.QFR.GKSPIL
Retrocopy DKRSFLLDLLCATGKDSLTLVFVETKKGADSLEDFLYHEGFACASIHGDRSQRDREEALRQFRLGKSPIL

Parental  VATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNVNITKDLLDLLVEAKQ
          VATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERN.NITKDLLDLL.EAKQ
Retrocopy VATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVGNLGLATSFFNERNANITKDLLDLLIEAKQ

Parental  EVPSWLENMAFEHHYKGGSRGRSKSSRFSGGFGARDYRQSSGAGSSSFSSSRASSSRSGGGGHGGSRGFG
          EVPSWL.NMAFEHH.KG.SRGRSK.SRF.GGFG.RDYRQ.SG.GSS.....RASSSRSGGG.HG.SRGFG
Retrocopy EVPSWLKNMAFEHHHKGSSRGRSK-SRFTGGFGGRDYRQNSGSGSS--CNNRASSSRSGGGSHGNSRGFG

Parental  GGGYGGFYNSDGYGGNYNSQGVDWWGN
          GGGYGGFY.SDGYGGNYNSQ.VDWWGN
Retrocopy GGGYGGFYSSDGYGGNYNSQSVDWWGN

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	0.29 RPM	121.82 RPM
SRP017611_kidney	0.21 RPM	173.36 RPM
SRP017611_liver	0.09 RPM	117.00 RPM
SRP040447_lung	1.29 RPM	200.38 RPM
SRP040447_skeletal_muscle	0.31 RPM	91.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_53 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_53 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53 ,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898, retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415,