RetrogeneDB ID: retro_cpor_326

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_127:1358243..1359412(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_cpor_326
GAAAATGCGCTCGGGCTGGACCAGCAGTTTGCTGGCCTAGACCTGAACTCTTCAGATAATCAGACTGGAGGGAGTACGGC
CAGTAAGGGACGTTACATTCCTCCACATTTAAGGAACAGAGAAGCTACTAAAGGATACTACGACAAAGACAGTTCAGAGT
GGAGTTCTAGTAAGATAAGGATGCATACAGCAGTTTTGGATCCCGTAGTGATTCAAGAGGGAAGTCTAGTTTCTTCAGTG
ATTGTGGGAGTGGATCAAGGGGAAGATTTGATGATCGTGGACGGGGTGACTATGATGGCATTGGCAGCCGTGGAGACAGG
GGTGGCTTCAGCAAATTTGAACGTGGTGGAAACAGGTGCTGGTGTGACAAATCAGATGAAGGTGACCAGTCAAAACCACT
CCCACCAAGTGAACGCTTGGAGCAGGAACTCTTCTCTTGAGGCAACACTGGGATTAACTTTGAGAAATATGACGACATTC
CAGTTGAGGCAACAGGCAACAAACTGTCCTCCACATAGTGAAAGTTTCAGTGATGTCGAGATGGGAGAAATTGTTATGGG
AAACATTGAGCTTACTTGTTATACTCGCCCAACTCCAGGGCAGAAGCATGCTATTACTATTATCAAAGAGAAAAGAGACT
TGATGGCTTGTGCCCAAACAGGGTCTGGAAAAACTGCAGCATTTCTGTTGCCCATCTCGAGTCAGATTTATTCAGATGGT
CCTGGTGAAGCTTTGAGGGCCATGAAGGAAAATGGAAGGTATGGGCGCTGCAAACAATACCCAATCTCCTTGATGTTGGT
ACCAACCAGAGAGTTGGCAGTACAGACCTATAAAGAAGCCAGAAAATTCTCATACCGATCTAGAATCCGTCCTTGTGTGG
TTTATGGTGGTGCTGATACTGGTCAGCAGATTTGAGACTTAGAACGTGGTTGCCACTTGTTAGTAGCTACTCCAGGACAT
CTTGTGGATATGATGGAAAGAGGAAAGATTGGATTAGACTTCTGCAAGTACTTGGTGTTGGATGAGGCTGATCGGATGTT
GGATATGGGGCTTGAACCTCAGATACATAGAACTGTGGAGCAAGATACTATGCCTCCCAAGGTGTCCATCACACTATGGT
GTTTAGTGCTACTTTTCCTAAGGAAATACAGATGCTGGCTCATGACTAC

Alignment

ORF - retro_cpor_326 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 59.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ENALGLDQQFAGLDLNSSDNQTGGSTASKGRYIPPHLRNREATKGYYDKDSSGWSSSK-DKDAYSSFGSR
          ENALGLDQQFAGLDLNSSDNQTGGSTASKGRYIPPHLRNREATKGYYDKDSS.WSSSK.DKDAYSSFGSR
Retrocopy ENALGLDQQFAGLDLNSSDNQTGGSTASKGRYIPPHLRNREATKGYYDKDSSEWSSSK<DKDAYSSFGSR

Parental  NDSRGKSSFFSDRGSGSRGRFDDRGRGDYDGIGSRGDRGGFGKFERGGNSRWCDKSDEDDWSKPLPPSER
          .DSRGKSSFFSD.GSGSRGRFDDRGRGDYDGIGSRGDRGGF.KFERGGN..WCDKSDE.D.SKPLPPSER
Retrocopy SDSRGKSSFFSDCGSGSRGRFDDRGRGDYDGIGSRGDRGGFSKFERGGNRCWCDKSDEGDQSKPLPPSER

Parental  LEQELFSGGNTGINFEKYDDIPVEATGN-NCPPHIESFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPII
          LEQELFS.GNTGINFEKYDDIPVEATGN.NCPPH.ESFSDVEMGEI.MGNIELT.YTRPTP.QKHAI.II
Retrocopy LEQELFS*GNTGINFEKYDDIPVEATGN>NCPPHSESFSDVEMGEIVMGNIELTCYTRPTPGQKHAITII

Parental  KEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYE
          KEKRDLMACAQTGSGKTAAFLLPI.SQIYSDGPGEALRAMKENGRYGR.KQYPISL.L.PTRELAVQ.Y.
Retrocopy KEKRDLMACAQTGSGKTAAFLLPISSQIYSDGPGEALRAMKENGRYGRCKQYPISLMLVPTRELAVQTYK

Parental  EARKFSYRSRVRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLD
          EARKFSYRSR.RPCVVYGGAD.GQQI.DLERGCHLLVATPG.LVDMMERGKIGLDFCKYLVLDEADRMLD
Retrocopy EARKFSYRSRIRPCVVYGGADTGQQI*DLERGCHLLVATPGHLVDMMERGKIGLDFCKYLVLDEADRMLD

Parental  MGFEPQIRRIVEQDTMPPK-GVRHTMMFSATFPKEIQMLARDF
          MG.EPQI.R.VEQDTMPPK.GV.HTM.FSATFPKEIQMLA.D.
Retrocopy MGLEPQIHRTVEQDTMPPK<GVHHTMVFSATFPKEIQMLAHDY

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	0.12 RPM	121.82 RPM
SRP017611_kidney	0.21 RPM	173.36 RPM
SRP017611_liver	0.17 RPM	117.00 RPM
SRP040447_lung	3.18 RPM	200.38 RPM
SRP040447_skeletal_muscle	1.42 RPM	91.11 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_326 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_326 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,