RetrogeneDB ID: retro_cpor_503

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_17:32918203..32918770(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AUH
• Ensembl ID: ENSCPOG00000001066
• Aliases: None
• Description: None

Sequence

>retro_cpor_503
AGGAGAATTGTGATGCTTGGAATAAACAGAGCTTAAGGCAAGAATTCACTCAGCTAAAATCTTATAAAAATGTTATCAAA
AACTGTGGATGCTTTAAACTCTTCAAAGAAAATTCAGGCCATAATAATAGGGAGCGAAGTCCCAGGGATATTCTGTACTG
GTGCTGACCTTGAGGAAAGAGCAGAAATGCATCCCAGTGAAGTTGGTCCTGTTGTCTCCAGAGTCACCAGAATCAGAGCA
GAGGATAATGACATAGGTAAGCTGCCTGTGCTCACAGTTGCAGCCATAGATGGACTCATTTTAGGTGGGGTCCTGGACTG
GCTTTCTCATGTGACGTAGGAACAGCCACTTCCTCCGCAAAACAGGGCCTGGTTGGAAACAAAGTTGGCGATTATTGCTG
GTGGAGGGATGCAGCAATTACTGCGTGCCATTGGAACGTCCCTGACCAAGGAGCTTATTTCCTCGGCATGAGTGTTTGAT
GGCCAAGAAGCCAAAGCTGTGGGCCTGGCCAGCCTCATGCAAGGGCAGAACCAGAAGGGTGATGCCACCTACAGAAGGGC
CCTGGAC

Alignment

ORF - retro_cpor_503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.27 %
• Parental protein coverage: 71.92 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RGILVLGINRAYAKNSLSKNLVKTLSKTVDALKSDKKVRTIIIRSEVPGIFCAGADLKERAKMHPSEVGP
          R.I..LGINRA..KNSLS.NL.K.LSKTVDAL.S.KK...III.SEVPGIFC.GADL.ERA.MHPSEVGP
Retrocopy RRIVMLGINRA*GKNSLS*NLIKMLSKTVDALNSSKKIQAIIIGSEVPGIFCTGADLEERAEMHPSEVGP

Parental  FVS---KIRAVINDIANLPVPTIAAIDGLALGGGLE-LALACDIRVAASSAKMGLV-ETKLAIIPGGGGT
          .VS....IRA..NDI..LPV.T.AAIDGL.LGG.L..LA..CD...A.SSAK.GLV.ETKLAII..GGG.
Retrocopy VVSRVTRIRAEDNDIGKLPVLTVAAIDGLILGGVLD<LAFSCDVGTATSSAKQGLV>ETKLAII-AGGGM

Parental  QRLPRAIGMSLAKELIFSARVLDGQEAKAVGLVSHVLEQNPEGDAAYRKALD
          Q.L.RAIG.SL.KELI.SA.V.DGQEAKAVGL.S....QN..GDA.YR.ALD
Retrocopy QQLLRAIGTSLTKELISSA*VFDGQEAKAVGLASLMQGQNQKGDATYRRALD

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	23.41 RPM
SRP017611_kidney	0.00 RPM	46.06 RPM
SRP017611_liver	0.00 RPM	42.44 RPM
SRP040447_lung	0.00 RPM	14.98 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.14 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_503 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_503 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005695	1 retrocopy	retro_cjac_93,
Cavia porcellus	ENSCPOG00000001066	1 retrocopy	retro_cpor_503 ,
Oreochromis niloticus	ENSONIG00000011227	1 retrocopy	retro_onil_68,
Pan troglodytes	ENSPTRG00000021099	1 retrocopy	retro_ptro_1612,