RetrogeneDB ID: retro_cpor_1518

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_91:6192523..6193255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR2B
• Ensembl ID: ENSCPOG00000002372
• Aliases: None
• Description: None

Sequence

>retro_cpor_1518
TCAGTATGTACAAAAGCATATAACCCTGATGAAGAAGATGTTGCAGAGTCCAGGATTACACATCCAAAAATCAATGATCA
AAGAAATAGATTGCAAGAAGCTTACAAAGACATCCTGCTCTTTAAGAACATGGATCCAGAACAGATGTCTCAAGTATTAG
ATGCCATGTTTGAAAAACTGGTCAAAAAATGGAACCATGTAATTGATCAAGGAGATGACAGTGACAACTTTTATGTAACT
GATAGATGAACTTTTGATATTTATATAAAATGTGATGGTGTTGGAAGATGAGTTGGTAATTGTGACAATTGTGGGAGTTT
GGGTGAACAGGCTTTAATGTACAACACACCCAGAGCAGCTACACTCACAGCTAACTCTCCTGGTGCTTTGTGTGGTTTGG
ACAGGGTAACTTCAGGAGAATAATTGTAAAAAACAATATCAAAAGAGAAAAATGCATGAAAGCTTTATTGAGTCTCTGCC
ATTCCTTAAATCTCTGAAGTCCCTGAAGGCCTAAAACTGGTAGATCTGATAGGCACCAAAGTATAGAACAATGGAGAACA
AATCATTTCTCAGGGAGATTTGGCTGATTCTTTTTTCATTGTAGTATTTGGAGAAGTAAAAATTACTATGAATAGAAAGG
GAAAATCAGAAGTGGAAGAGAACGGTGCAATAGAAATTGGTCAATGTTCCTGGGAATAGTACTTTAGAGAGCTTGCCAAC
AAACCTCGAGCC

Alignment

ORF - retro_cpor_1518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.76 %
• Parental protein coverage: 69.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVCAEAYNPDEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID
          SVC..AYNPDEE.D.AESRI.HPK..DQRNRLQEA.KDILLFKN.DPEQMSQVLDAMFEKLVK...HVID
Retrocopy SVCTKAYNPDEE-DVAESRITHPKINDQRNRLQEAYKDILLFKNMDPEQMSQVLDAMFEKLVKKWNHVID

Parental  QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGELALMYNTPRAATITATSPGALWGLDRVT-F
          QGDD.DNFYV.DR.TFDIY.KCDGVGR.VGN.DN.GS.GE.ALMYNTPRAAT.TA.SPGAL.GLDRVT.F
Retrocopy QGDDSDNFYVTDR*TFDIYIKCDGVGR*VGNCDNCGSLGEQALMYNTPRAATLTANSPGALCGLDRVT<F

Parental  RRIIVKNNAK-KRKMYESFIESLPFLKSL-EVSERLKVVDVIGTKVYSDGEQIIAQGDLADSFFIVESGE
          RRIIVKNN.K.KRKM.ESFIESLPFLKSL.EV.E.LK.VD.IGTKV...GEQII.QGDLADSFFIV..GE
Retrocopy RRIIVKNNIK<KRKMHESFIESLPFLKSL<EVPEGLKLVDLIGTKV*NNGEQIISQGDLADSFFIVVFGE

Parental  VKITMKRKGKSEAEENGAVEIARCSRGQYFGELALVTNKPRA
          VKITM.RKGKSE.EENGA.EI..CS...YF.ELA...NKPRA
Retrocopy VKITMNRKGKSEVEENGAIEIGQCSWE*YFRELA---NKPRA

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	50.04 RPM
SRP017611_kidney	0.00 RPM	42.61 RPM
SRP017611_liver	0.00 RPM	19.06 RPM
SRP040447_lung	0.03 RPM	51.58 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.88 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1518 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1518 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002372	1 retrocopy	retro_cpor_1518 ,
Oryctolagus cuniculus	ENSOCUG00000012747	1 retrocopy	retro_ocun_1288,