RetrogeneDB ID:

retro_ocun_1132

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:20:7975384..7975934(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000027752
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1B
Ensembl ID:ENSOCUG00000029552
Aliases:None
Description:RAP1B, member of RAS oncogene family [Source:HGNC Symbol;Acc:9857]


Retrocopy-Parental alignment summary:






>retro_ocun_1132
ATGCGTGAATATACACCAGTCATTCTTGGTTCAAGAGGTGTTGAAAAGTCTGCTCTGACTGTACAGTTTGTTCAAGGAAT
TTTTGTTGAAAATATGATCCTACAATAGAAGATTCTTATGGGAAGCGAGTTGCGGTAAGTGCCCAACAATGTACCTTAAA
ATCTTGGATACTGCCGGAATGGAACAATTTACAACAGTGAGGGATCTGTACGTGAAAAGTGGACCAGACTCTGCATTAGT
TCATTTCATCACAGCACAGTCTACATGGAATGACCTACAGGACCTGAGAGAGCAGATTCTTCAAGTTAGAGACACTGATG
ATGTTCCGGCGATTCTGGCTGGTAGTAAGTGTGACTTGGAAGATCAAAGAGTTGCAGGAAAGGAAAGAGGTCAAAATCCA
GCAAGACAACAGAACAACTGTGCATTCTTAAATACTCTGCAAAATCAAAAATAAATGTTAATGACTTCTTTTATGACCTG
GTGCAGTGAATTAATGGAAGAACACCAGTGCCTGGGAAGGCCCAGGGAAAAGTCATCGTGTTCTCTGCTT

ORF - retro_ocun_1132 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.53 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 1
Number of frameshifts detected: 4


Retrocopy - Parental Gene Alignment:

ParentalMREYKLVVLGSGGVGKSALTVQFVQGIFVE-KYDPTIEDSYRKQVEVDAQQCMLE-ILDTAGTEQFTAMR
MREY..V.LGS.GV.KSALTVQFVQGIFVE.KYDPTIEDSY.K.V.V.AQQC.L..ILDTAG.EQFT..R
RetrocopyMREYTPVILGSRGVEKSALTVQFVQGIFVE<KYDPTIEDSYGKRVAVSAQQCTLK<ILDTAGMEQFTTVR
ParentalDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQW
DLY.K.G...ALV..ITAQST.NDLQDLREQIL.V.DTDDVP.IL.G.KCDLED.RV.GKE.GQN.ARQ.
RetrocopyDLYVKSGPDSALVHFITAQSTWNDLQDLREQILQVRDTDDVPAILAGSKCDLEDQRVAGKERGQNPARQQ
ParentalNNCAFLES-SAKSKINVNEIFYDLVRQINRKTPVPGKA-RKKSSCQLL
NNCAFL...SAKSKINVN..FYDLV..IN..TPVPGKA.R.KSSC.LL
RetrocopyNNCAFLNT<SAKSKINVNDFFYDLVQ*INGRTPVPGKA>REKSSCSLL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP017611_brain 0 .00 RPM 47 .19 RPM
SRP017611_kidney 0 .00 RPM 67 .71 RPM
SRP017611_liver 0 .00 RPM 20 .81 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1132 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1132 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1132 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 17 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
retro_amel_103,
Cavia porcellus ENSCPOG000000082724 retrocopies
retro_cpor_1194, retro_cpor_632, retro_cpor_739, retro_cpor_85,
Dasypus novemcinctus ENSDNOG0000001972418 retrocopies
retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Erinaceus europaeus ENSEEUG000000100521 retrocopy
retro_eeur_327,
Echinops telfairi ENSETEG000000002421 retrocopy
retro_etel_11,
Gorilla gorilla ENSGGOG000000256491 retrocopy
retro_ggor_2836,
Loxodonta africana ENSLAFG000000164601 retrocopy
retro_lafr_482,
Microcebus murinus ENSMICG000000131481 retrocopy
retro_mmur_116,
Macaca mulatta ENSMMUG000000114422 retrocopies
retro_mmul_1151, retro_mmul_1863,
Oryctolagus cuniculus ENSOCUG000000224551 retrocopy
retro_ocun_850,
Oryctolagus cuniculus ENSOCUG00000029552 5 retrocopies
retro_ocun_1132 , retro_ocun_1200, retro_ocun_597, retro_ocun_636, retro_ocun_796,
Otolemur garnettii ENSOGAG000000057462 retrocopies
retro_ogar_2260, retro_ogar_272,
Pongo abelii ENSPPYG000000047511 retrocopy
retro_pabe_3403,
Pan troglodytes ENSPTRG000000051973 retrocopies
retro_ptro_1812, retro_ptro_2383, retro_ptro_2877,
Rattus norvegicus ENSRNOG000000070484 retrocopies
retro_rnor_2479, retro_rnor_870, retro_rnor_871, retro_rnor_872,
Sus scrofa ENSSSCG000000211481 retrocopy
retro_sscr_1125,
Sus scrofa ENSSSCG000000300142 retrocopies
retro_sscr_435, retro_sscr_909,


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