RetrogeneDB ID:

retro_ocun_10

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:2:116117550..116118621(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000003634
Aliases:PCBP1, hnRNP E1
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000022490
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_10
ATGGATGCCGGTGTGACTGAAAGCGGACTAAATGTGACTCTCACCATTCGGCTTCTTATGCACGGAAAGGAAGTAGGAAG
CATCATTGGGAAGAAAGGGGAGTCGGTTAAGAGGATCCGCGAGGAGAGTGGCGCGCGGATCAACATCTCGGAGGGGAATT
GTCCGGAGCGAATCATCACTCTGACCGGCCCCACTAATGCCATCTTCAAGGCATTCGCTATGATCATCGACAAGCTGGAG
GAAGATATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCCGGCCCCCGGTGACCCTGCGGCTGGTGGTGCCGGCCAC
CCAGTGCGGCTCCCTGATCGGGAAAGGCGGGTGTAAGATCAAAGAGATCCGCGAGAGCACGGGGGCCCAGGTCCAGGTGG
CGGGGGATATGCTGCCCAACTCGACCGAGCGGGCCATCACCATCGCGGGCGTGCCGCAGTCTGTCACCGAGTGTGTCAAG
CAGATCTGCCTGGTCATGCTGGAGACGCTCTCCCAGTCTCCGCAAGGGAGAGTCATGACCATTCCGTACCAGCCCATGCC
GGCCAGCTCTCCGGTCATCTGCGCGGGCGGCCAAGATCGCTGCAGCGACGCTGCGGGCTACCCCCACGCCACCCATGACC
TGGAGGGACCACCTCTAGATGCCTACTCGATTCAAGGACAACACACCATTTCTCCGCTCGATCTGGCCAAGCTGAACCAG
GTGGCAAGACAACAGTCTCACTTTGCCATGATGCACGGCGGGACCGGATTCGCCGGAATTGACTCCAGCTCTCCAGAGGT
GAAAGGCTATTGGGCAAGTTTGGATGCATCTACTCAAACCACCCATGAACTCACCATTCCAAATAACTTAATTGGCTGCA
TAATCGGGCGCCAAGGCGCCAACATTAATGAGATCCGCCAGATGTCGGGGGCCCAGATCAAAATTGCCAACCCAGTGGAA
GGCTCTTCTGGTAGGCAGGTTACTATCACTGGCTCTGCTGCCAGTATTAGTCTGGCCCAGTATCTAATCAATGCCAGGCT
TTCCTCTGAGAAGGGCATGGGGTGCAGCTAG

ORF - retro_ocun_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.18 %
Parental protein coverage: 98.34 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMDTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
MD.GV.E.GLNVTLTIRLLMHGKEVGSIIGKKGESVK..REESGARINISEGNCPERIITL.GPTNAIFK
RetrocopyMDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGPTNAIFK
ParentalAFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
AFAMIIDKLEEDI.SSMTNSTAASRPPVTLRLVVPA.QCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
RetrocopyAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
ParentalSTERAITIAGIPQSIIECVKQICVVMLETLSQSPP-KGVTIPYRPKPSSSPVIFAGGQQTPVCCSPDSQP
STERAITIAG.PQS..ECVKQIC.VMLETLSQSP.....TIPY.P.P.SSPVI.AGGQ.....CS.D...
RetrocopySTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPASSPVICAGGQDR---CS-DAAG
ParentalQKHCWHELEQTPTRAYTIQGQYAIPQPDLTKLHQLAMQQSHFPMTHGNTGFSGIESSSPEVKGYWAGLDA
..H..H.LE..P..AY.IQGQ..I...DL.KL.Q.A.QQSHF.M.HG.TGF.GI.SSSPEVKGYWA.LDA
RetrocopyYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTGFAGIDSSSPEVKGYWASLDA
ParentalSAQTTSHELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLINV
S.QTT.HELTIPN.LIGCIIGRQGA.INEIRQMSGAQIKIANPVEGS..RQVTITGSAASISLAQYLIN.
RetrocopySTQTT-HELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVEGSSGRQVTITGSAASISLAQYLINA
ParentalSRRSNQ
...S..
RetrocopyRLSSEK

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 178 .64 RPM 82 .67 RPM
SRP017611_kidney 241 .33 RPM 104 .60 RPM
SRP017611_liver 105 .21 RPM 61 .66 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_10 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_10 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_10 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_175
Sus scrofa retro_sscr_61
Equus caballus retro_ecab_67
Pongo abelii retro_pabe_92
Parental genes homology:
Parental genes homology involve 26 parental genes, and 59 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207571 retrocopy
retro_btau_175,
Canis familiaris ENSCAFG000000068211 retrocopy
retro_cfam_54,
Callithrix jacchus ENSCJAG000000185902 retrocopies
retro_cjac_3253, retro_cjac_754,
Cavia porcellus ENSCPOG000000009672 retrocopies
retro_cpor_193, retro_cpor_97,
Dasypus novemcinctus ENSDNOG000000086886 retrocopies
retro_dnov_1146, retro_dnov_1399, retro_dnov_1672, retro_dnov_1823, retro_dnov_2434, retro_dnov_452,
Equus caballus ENSECAG000000223891 retrocopy
retro_ecab_67,
Erinaceus europaeus ENSEEUG000000010772 retrocopies
retro_eeur_218, retro_eeur_655,
Echinops telfairi ENSETEG000000147413 retrocopies
retro_etel_1170, retro_etel_2108, retro_etel_840,
Homo sapiens ENSG000001971112 retrocopies
retro_hsap_4077, retro_hsap_83,
Gorilla gorilla ENSGGOG000000126132 retrocopies
retro_ggor_212, retro_ggor_2734,
Macropus eugenii ENSMEUG000000018877 retrocopies
retro_meug_1143, retro_meug_1988, retro_meug_432, retro_meug_526, retro_meug_618, retro_meug_828, retro_meug_964,
Microcebus murinus ENSMICG000000116512 retrocopies
retro_mmur_1226, retro_mmur_1228,
Myotis lucifugus ENSMLUG000000099713 retrocopies
retro_mluc_2199, retro_mluc_314, retro_mluc_571,
Macaca mulatta ENSMMUG000000066082 retrocopies
retro_mmul_1263, retro_mmul_1994,
Mus musculus ENSMUSG000000568511 retrocopy
retro_mmus_274,
Nomascus leucogenys ENSNLEG000000176931 retrocopy
retro_nleu_10,
Oryctolagus cuniculus ENSOCUG000000026961 retrocopy
retro_ocun_1257,
Oryctolagus cuniculus ENSOCUG00000022490 3 retrocopies
retro_ocun_10 , retro_ocun_1622, retro_ocun_898,
Ochotona princeps ENSOPRG000000046805 retrocopies
retro_opri_1126, retro_opri_284, retro_opri_313, retro_opri_742, retro_opri_789,
Pongo abelii ENSPPYG000000045812 retrocopies
retro_pabe_3346, retro_pabe_92,
Pan troglodytes ENSPTRG000000050181 retrocopy
retro_ptro_113,
Pteropus vampyrus ENSPVAG000000122843 retrocopies
retro_pvam_1168, retro_pvam_1369, retro_pvam_868,
Rattus norvegicus ENSRNOG000000368522 retrocopies
retro_rnor_1238, retro_rnor_2088,
Sus scrofa ENSSSCG000000002741 retrocopy
retro_sscr_61,
Ictidomys tridecemlineatus ENSSTOG000000036352 retrocopies
retro_itri_1522, retro_itri_557,
Vicugna pacos ENSVPAG000000004061 retrocopy
retro_vpac_471,


Copyright © RetrogeneDB 2014-2017