RetrogeneDB ID:

retro_ocun_1315

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:7:101845320..101846162(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000027169
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSOCUG00000000270
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ocun_1315
TCGAGGATGTCGGATGAGGAGAAGGTACGCAAAGCTGCTAAATTCATCACTCATGCACCCCCAGGAGAATTTAATGAAGT
ATTGAATGATGTCCGACTACTACTTAATAATGACAATCTCCTCAGGGAAGGGGCAGCACATGCATTTGCCCAGTATAACA
TGGATCAGTTCACGCCTGTCAAGATAGAAGGATATGAAGATCAGGTCTTAATTACAGAGCACGGTGACCTGGGTAATAGC
AGATTTTTAGATCCAAGAAACAAAATTTCCTTTAAGTTTGATCACTTACGGAAAGAAGCAAGTGATCCCCAGCCAGAGGA
AGTAGATGGAGGCTTGAAGTCGTGGAGAGAATCCTGTGACAGTGCTTTGAGAGCCTATGTGAAAGATCATTATTCCAACG
GCTTCTGTACTGTGTATGCTAAAACTATAGATGGGCAGCAGACTATTATTGCATGTATTGAAAGCCACCAATTTCAGCCT
AAAAACTTCTGGAATGGTCGTTGGAGATCAGGGTGGAAATTCACCATCACACCACCTACAGCCCAAGTGGTTGGAGTGCT
TAAGATTCAGGTTCACTATTACGAAGATGGCAATGTTCAGTTGGTTAGTCATAAAGATGTACAAGACTCAATAACTGTGT
CGAATGAAATACAAACTGCCAAGGAGTTTATTAAAATCATAGAGAATGCAGAAAATGAATATCAGACGGCAATTAGTGAA
AACTATCAAACCATGTCAGACACCACATTCAAGGCCTTGCGCCGGCAACTTCAGTTACCCGCACCAAAATCGACTGGAGC
AAGATACTCAGCTACAAGATTGGCAAAGAAATGCAGAATGCT

ORF - retro_ocun_1315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.41 %
Parental protein coverage: 98.26 %
Number of stop codons detected: 0
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalTRNSHGCSVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVL
.R.S....VR.AAKFITHAPPGEFNEV.NDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVL
RetrocopySRMSDEEKVRKAAKFITHAPPGEFNEVLNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQVL
ParentalITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTVVY
ITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTV.Y
RetrocopyITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVDGGLKSWRESCDSALRAYVKDHYSNGFCTV-Y
ParentalAKTIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQD
AKTIDGQQTIIACIESHQFQPKNFWNGRWRS.WKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQD
RetrocopyAKTIDGQQTIIACIESHQFQPKNFWNGRWRSGWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQD
ParentalSITVSNEIQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQL-PVTRTKIDWNKILSYKIGKEM
SITVSNEIQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQL..VTRTKIDW.KILSYKIGKEM
RetrocopySITVSNEIQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQL<SVTRTKIDWSKILSYKIGKEM
ParentalQNA
QNA
RetrocopyQNA

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 2 .70 RPM 20 .70 RPM
SRP017611_kidney 2 .33 RPM 21 .99 RPM
SRP017611_liver 1 .39 RPM 13 .72 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_1315 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1315 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_1315 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000035701 retrocopy
retro_amel_219,
Choloepus hoffmanni ENSCHOG000000041318 retrocopies
retro_chof_1008, retro_chof_1419, retro_chof_1499, retro_chof_1704, retro_chof_1861, retro_chof_2129, retro_chof_625, retro_chof_711,
Callithrix jacchus ENSCJAG000000135483 retrocopies
retro_cjac_2259, retro_cjac_2850, retro_cjac_4125,
Cavia porcellus ENSCPOG000000145321 retrocopy
retro_cpor_1155,
Dipodomys ordii ENSDORG000000006713 retrocopies
retro_dord_224, retro_dord_265, retro_dord_44,
Felis catus ENSFCAG000000133032 retrocopies
retro_fcat_700, retro_fcat_746,
Homo sapiens ENSG000001164892 retrocopies
retro_hsap_2338, retro_hsap_4871,
Gorilla gorilla ENSGGOG000000236771 retrocopy
retro_ggor_1216,
Latimeria chalumnae ENSLACG000000179631 retrocopy
retro_lcha_20,
Myotis lucifugus ENSMLUG000000097961 retrocopy
retro_mluc_2483,
Macaca mulatta ENSMMUG000000156682 retrocopies
retro_mmul_2612, retro_mmul_942,
Mustela putorius furoENSMPUG000000049771 retrocopy
retro_mputfur_616,
Mus musculus ENSMUSG000000703724 retrocopies
retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Nomascus leucogenys ENSNLEG000000041911 retrocopy
retro_nleu_1689,
Oryctolagus cuniculus ENSOCUG00000000270 6 retrocopies
retro_ocun_1315 , retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Oryctolagus cuniculus ENSOCUG000000035912 retrocopies
retro_ocun_1531, retro_ocun_873,
Otolemur garnettii ENSOGAG000000140744 retrocopies
retro_ogar_1640, retro_ogar_2159, retro_ogar_3217, retro_ogar_845,
Pongo abelii ENSPPYG000000010212 retrocopies
retro_pabe_2116, retro_pabe_3789,
Pan troglodytes ENSPTRG000000011102 retrocopies
retro_ptro_1710, retro_ptro_3245,
Rattus norvegicus ENSRNOG000000135381 retrocopy
retro_rnor_77,
Sorex araneus ENSSARG000000012781 retrocopy
retro_sara_166,
Ictidomys tridecemlineatus ENSSTOG000000159561 retrocopy
retro_itri_1044,
Tupaia belangeri ENSTBEG000000017275 retrocopies
retro_tbel_1870, retro_tbel_3525, retro_tbel_4327, retro_tbel_638, retro_tbel_868,
Tarsius syrichta ENSTSYG000000062592 retrocopies
retro_tsyr_179, retro_tsyr_471,
Vicugna pacos ENSVPAG000000053611 retrocopy
retro_vpac_579,


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