RetrogeneDB ID: retro_ocun_1288

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:8136187..8136829(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR2B
• Ensembl ID: ENSOCUG00000012747
• Aliases: None
• Description: protein kinase, cAMP-dependent, regulatory, type II, beta [Source:HGNC Symbol;Acc:9392]

Sequence

>retro_ocun_1288
TGTGACGGTGTGGGAAGATGTGTTGGCAACCACGATAACTGTGGGAGTTTCGGCGAGCTGGCCTTAATGTACAACACACC
CAGAGCAGCTACAATCACTGCTACCTCTCCTGGTACTCTATGGGGCCCGGACAGGGTAACCTTCAGGAGGATAATTGTGA
AAAATAATGCCAAAAAGAGGAAAATGTATGAAAGCTTTATCGAGTCACTGCCGTTCTTCAAATTCCTGGAGGTTCCTGAA
TGCCCAAAAGTGGTAGATGTGATTGGCACCAAAGTATACAATGATGGAGAACAGATCATTGCTCAGGGAGATCTTGCGGA
TTCTTTTTTCATTGTAGAATCTGGAGAGGTGAAAATTACCATGAAGAGAAAGGGCAAGTCCGAAGTGGAAGAGAAGGGCG
TGGTGGAAATCGCTGGCTGCTCCCGGGGACAGTACTTTGGAGAGCTCTCCCTGGTGACGAACAAGCCTTGAGCAGCCTTG
GCGCACGCCATTGGGACCGTCAAATGCCTGGCCATGGATGTGAAAGTGTTTGAGAGGCTCTTGGGACCTTGCATGGAGAT
CATGAAAAGGAACATAGCCACGTATGAAGAGCAGTTAGTGGCGCTGCTTGGAACAAACATGGATATTGTTGAACCTACTG
CA

Alignment

ORF - retro_ocun_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.59 %
• Parental protein coverage: 50.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CDGVGRCVGNYDNRGSFGELALMYNTPRAATITATSPGALWGLDRVTFRRIIVKNNAKKRKMYESFIESL
          CDGVGRCVGN.DN.GSFGELALMYNTPRAATITATSPG.LWG.DRVTFRRIIVKNNAKKRKMYESFIESL
Retrocopy CDGVGRCVGNHDNCGSFGELALMYNTPRAATITATSPGTLWGPDRVTFRRIIVKNNAKKRKMYESFIESL

Parental  PFLKSLEVSERLKVVDVIGTKVYNDGEQIIAQGDLADSFFIVESGEVKITMKRKGKSEVEENGAVEIARC
          PF.K.LEV.E..KVVDVIGTKVYNDGEQIIAQGDLADSFFIVESGEVKITMKRKGKSEVEE.G.VEIA.C
Retrocopy PFFKFLEVPECPKVVDVIGTKVYNDGEQIIAQGDLADSFFIVESGEVKITMKRKGKSEVEEKGVVEIAGC

Parental  SRGQYFGELALVTNKPRAASAHAIGTVKCLAMDVQAFERLLGPCMEIMKRNIATYEEQLVALFGTNMDIV
          SRGQYFGEL.LVTNKP.AA.AHAIGTVKCLAMDV..FERLLGPCMEIMKRNIATYEEQLVAL.GTNMDIV
Retrocopy SRGQYFGELSLVTNKP*AALAHAIGTVKCLAMDVKVFERLLGPCMEIMKRNIATYEEQLVALLGTNMDIV

Parental  EPTA
          EPTA
Retrocopy EPTA

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	18.98 RPM
SRP017611_kidney	0.00 RPM	3.04 RPM
SRP017611_liver	0.00 RPM	0.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1288 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1288 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1288 has 0 orthologous retrocopies within eutheria group .

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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	ENSCPOG00000002372	1 retrocopy	retro_cpor_1518,
Oryctolagus cuniculus	ENSOCUG00000012426	1 retrocopy	retro_ocun_538,
Oryctolagus cuniculus	ENSOCUG00000012747	1 retrocopy	retro_ocun_1288 ,