RetrogeneDB ID: retro_ocun_538

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:137186011..137187020(+)
• Located in intron of: ENSOCUG00000006898

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKAR2A
• Ensembl ID: ENSOCUG00000012426
• Aliases: None
• Description: protein kinase, cAMP-dependent, regulatory, type II, alpha [Source:HGNC Symbol;Acc:9391]

Sequence

>retro_ocun_538
CCTAGCCCAGTCCCAGTATCCGACAAGAATGCCACCAGCGACTCCGAGGAAGATGCAGACTTGGAAGTTCTGATTCCTAG
CATATTTGATAGACGAGCATCAGTCTGTGCTGAGGTGTATACCCCTGACGAAGAGGAAGAAGATAGAGACCCAAGGGTGA
TTCATCCTAAAACTTATGACTAGTGATGCAGACTTCAAGAACCTTGCAAAGATAGTCTCCTTTTCAAAAATCATGATCAG
AAATAACTTTCTCAAGTTCTTGATGCCATGTTTGAAAGGATAGTCTAATTGATGAACATGTCATTGATCAAGGAGATGAT
GGAGACGATTTTATGTCATAGAAAGGGGAACCTATGACATGTTGGTAACAAGAGATAAGCAAACATGCTCTTTTGGTCAG
TATGATAATCATGGCAGTTTTGGAGAGCTAGCCCTGATGTACAATACCCCAAGAGCTATTACCACTGCTGCTAATTCTGA
AGGCTTCCTTTGGGGACTGGACCAGGTGACTTTTAGAAGAAATATAGTGAAAAACAATGCAAAAAAGAAGATGTTTGAAT
CATTTATTGAGTCTGTCCCCTCCTTAAGTCACTACAGGTGTCGGAATGAATGAAGACTGTAGATGTCATTGGAGAGAAGG
TCTATAAGGATGGAGAATGCATAATTGCTCAGGTGAAAATGCTGATAGCATTTATATCACAGAATCTGGGGATGTGAGCA
TCTTGATTAAAAGCAAGATTAAATCAAACAAGGATGGTGGGAACCAGGAAGTTGAGATTGCCCACTGCCATAAGGGGCTG
TACTTTGGAGAGCTTGCACTAGTCACCAACAAACTCAGAGCTACTTTGGCTTATGCAGTTGGAGATGTCAAATGCTTAGT
TATGGATGTGCCAGCATTTGAGAGGCTTCTAGGGCCCTGCAAGGACATCATGAAGAGAAACATCTCACACTAGAAGAAAC
AGCTGGTAAGATATTTGGCTCCAACATGGATCTAATTGACCCTGGGCAA

Alignment

ORF - retro_ocun_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.56 %
• Parental protein coverage: 84.54 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PSPVPVADENADSDSEEDADLEVPIPSRFNRRVSVCAEAYNPDEEEEDTDPRVIHPKTDEQRCRLQESCK
          PSPVPV.D.NA.SDSEEDADLEV.IPS.F.RR.SVCAE.Y.PDEEEED.DPRVIHPKT....CRLQE.CK
Retrocopy PSPVPVSDKNATSDSEEDADLEVLIPSIFDRRASVCAEVYTPDEEEEDRDPRVIHPKTYD**CRLQEPCK

Parental  DILLFKNLDQEQLSQVLDAMFERIV-KVDEHVIDQGDDGDNF-YVIERGTYDILVTRDNQTRSVGQYDNH
          D.LLFKN.DQ..LSQVLDAMFERIV...DEHVIDQGDDGD.F.YVIERGTYD.LVTRD.QT.S.GQYDNH
Retrocopy DSLLFKNHDQK*LSQVLDAMFERIV<LIDEHVIDQGDDGDDF<YVIERGTYDMLVTRDKQTCSFGQYDNH

Parental  GSFGELALMYNTPRAATIVATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIESVP-LLKSLEVSERMK
          GSFGELALMYNTPRA.T..A.SEG.LWGLD.VTFRR.IVKNNAKK.KMFESFIESVP.LLKSL.VSE.MK
Retrocopy GSFGELALMYNTPRAITTAANSEGFLWGLDQVTFRRNIVKNNAKK-KMFESFIESVP<LLKSLQVSE*MK

Parental  IVDVIGEKVYKDGERIITQ-GEKADSFYIIESGEVSILIKSKTKSNKDGGNQEVEIARCHKGQYFGELAL
          .VDVIGEKVYKDGE.II.Q.GE.ADS.YI.ESG.VSILIKSK.KSNKDGGNQEVEIA.CHKG.YFGELAL
Retrocopy TVDVIGEKVYKDGECIIAQ<GENADSIYITESGDVSILIKSKIKSNKDGGNQEVEIAHCHKGLYFGELAL

Parental  VTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNISHYEEQLV-KIFGSSMDLIDPGQ
          VTNK.RA..AYAVGDVKCLVMDV.AFERLLGPC.DIMKRNISH...QLV.KIFGS.MDLIDPGQ
Retrocopy VTNKLRATLAYAVGDVKCLVMDVPAFERLLGPCKDIMKRNISH*KKQLV<KIFGSNMDLIDPGQ

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	57.78 RPM
SRP017611_kidney	0.00 RPM	121.02 RPM
SRP017611_liver	0.00 RPM	67.44 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_538 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_538 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_538 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003255	1 retrocopy	retro_cjac_1807,
Monodelphis domestica	ENSMODG00000013392	1 retrocopy	retro_mdom_97,
Oryctolagus cuniculus	ENSOCUG00000012426	1 retrocopy	retro_ocun_538 ,
Oryctolagus cuniculus	ENSOCUG00000012747	1 retrocopy	retro_ocun_1288,
Otolemur garnettii	ENSOGAG00000006822	1 retrocopy	retro_ogar_2423,