RetrogeneDB ID:

retro_ocun_1487

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:9:87962938..87963572(+)
Located in intron of:ENSOCUG00000011810
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000005150
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_1487
ATGTTGAGTGGGCGGCTGCCTCCTGACCTAAATGAAAATGATGTTGACTCAAACTCTAAAGATGAAGCCACACCAGATAA
CTCTGGACTTAACTCCCAGGAGGATGAAGAGGATGGGACCATTAAGAACACAGAAATCTCAGATTTCCCAACAGATGGAC
CAAAAACTGAAACAGAGATGATTGTAAATGCATATAAGGTATGTCCTTCTGGAATTCCCTTAAGACGTGGAATGAATTTC
AAGAAATGTATCAAAAACATCCTGAACAAAAAAATCTCAACCTCAAAATTCAGAGGGAAAAAAGAAACCATTTCAGAAAA
GATAAATTGAAGAATGGAAAACAATCTCCTGGCGAACAGTCCTCAAATGAAACCCCATGGAAAGAGCTTACTCAGTATTC
TGGAGTCAATGATTGATTTGAACCCTCTGTTAAAAAGGAAAAAGTTGAGGTATTGGGCTTTGAAAGGAGAATCAACCAGG
CTGTGGAGGAGTGGGAGGTTAAGAAGTCTGGGAGCTCGGCAACCAGCTAGCTATGTGCCGCGAGTTTGGTGTGAAAATTG
CCAAAGCAATTGCCTGCCACAAGTTTGTAAAAGCCAAAAAGGAGGCTGAAAATTCAAACTGTTCATAAAAAAAA

ORF - retro_ocun_1487 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.54 %
Parental protein coverage: 90.56 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMWSGLLPPGLNESDVESNSEDEAIPDNSGLNSQDGEEDGTIRNTEISNLPTDGPKAETETIVNAYEACPS
M.SG.LPP.LNE.DV.SNS.DEA.PDNSGLNSQ..EEDGTI.NTEIS..PTDGPK.ETE.IVNAY..CPS
RetrocopyMLSGRLPPDLNENDVDSNSKDEATPDNSGLNSQEDEEDGTIKNTEISDFPTDGPKTETEMIVNAYKVCPS
ParentalGIPLNM-WNKFQELHKKHSEQ-KISTSKFRGKK-RKRSRKDKLKNEKESHGEQSSNETQWKELTQYFGVN
GIPL...WN.FQE...KH.EQ.KISTSKFRGKK.R...RKDKLKN.K.S.GEQSSNET.WKELTQY.GVN
RetrocopyGIPLRR<WNEFQEMYQKHPEQ>KISTSKFRGKK<RNHFRKDKLKNGKQSPGEQSSNETPWKELTQYSGVN
ParentalDRFEPPVKKKKVEKSGLEKRIDQAVEEWDVEKAE-ELSNQLA-TRELGVKIAKAIACHKFVKAKKEAENS
D.FEP.VKK.KVE..G.E.RI.QAVEEW.V.K...EL.NQLA..RE.GVKIAKAIACHKFVKAKKEAENS
RetrocopyD*FEPSVKKEKVEVLGFERRINQAVEEWEVKKSG<ELGNQLAMCREFGVKIAKAIACHKFVKAKKEAENS
ParentalQAARKK
....KK
RetrocopyNCS*KK

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 87 .31 RPM
SRP017611_kidney 0 .00 RPM 35 .88 RPM
SRP017611_liver 0 .00 RPM 10 .10 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_1487 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1487 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1487 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000001019912 retrocopies
retro_chof_1296, retro_chof_1713, retro_chof_1977, retro_chof_2137, retro_chof_2367, retro_chof_2436, retro_chof_2558, retro_chof_2685, retro_chof_590, retro_chof_639, retro_chof_698, retro_chof_832,
Callithrix jacchus ENSCJAG000000195651 retrocopy
retro_cjac_3814,
Cavia porcellus ENSCPOG000000027471 retrocopy
retro_cpor_1356,
Dasypus novemcinctus ENSDNOG000000013832 retrocopies
retro_dnov_138, retro_dnov_167,
Dipodomys ordii ENSDORG000000020741 retrocopy
retro_dord_413,
Echinops telfairi ENSETEG000000038552 retrocopies
retro_etel_1021, retro_etel_944,
Homo sapiens ENSG000001656691 retrocopy
retro_hsap_491,
Gorilla gorilla ENSGGOG000000105661 retrocopy
retro_ggor_460,
Loxodonta africana ENSLAFG000000167744 retrocopies
retro_lafr_1079, retro_lafr_332, retro_lafr_369, retro_lafr_923,
Macropus eugenii ENSMEUG000000026741 retrocopy
retro_meug_606,
Myotis lucifugus ENSMLUG000000274541 retrocopy
retro_mluc_29,
Macaca mulatta ENSMMUG000000127411 retrocopy
retro_mmul_722,
Monodelphis domestica ENSMODG000000093783 retrocopies
retro_mdom_112, retro_mdom_1258, retro_mdom_38,
Mustela putorius furoENSMPUG000000032391 retrocopy
retro_mputfur_1400,
Oryctolagus cuniculus ENSOCUG00000005150 1 retrocopy
retro_ocun_1487 ,
Otolemur garnettii ENSOGAG000000285411 retrocopy
retro_ogar_1610,
Procavia capensis ENSPCAG000000115011 retrocopy
retro_pcap_400,
Pongo abelii ENSPPYG000000026941 retrocopy
retro_pabe_242,
Pan troglodytes ENSPTRG000000029841 retrocopy
retro_ptro_370,
Pteropus vampyrus ENSPVAG000000046212 retrocopies
retro_pvam_366, retro_pvam_776,
Sorex araneus ENSSARG000000008193 retrocopies
retro_sara_258, retro_sara_323, retro_sara_541,
Sarcophilus harrisii ENSSHAG000000116013 retrocopies
retro_shar_155, retro_shar_412, retro_shar_476,
Tarsius syrichta ENSTSYG000000091471 retrocopy
retro_tsyr_518,
Tursiops truncatus ENSTTRG000000033511 retrocopy
retro_ttru_1322,


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