RetrogeneDB ID:

retro_pabe_1371

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:16:4704974..4705355(-)
Located in intron of:ENSPPYG00000007063
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUB1
Ensembl ID:ENSPPYG00000015379
Aliases:SUB1, RPO2TC1
Description:Activated RNA polymerase II transcriptional coactivator p15 [Source:UniProtKB/Swiss-Prot;Acc:Q5R6D0]


Retrocopy-Parental alignment summary:






>retro_pabe_1371
ATGCCTAAATCAAAGGAACTTGTTTCTTCAAGCTCTTCTGGCAGTGATCCTGACAGTGAGGTTGACAAAAAGTTAAAGAG
GAAAAAGCAAGTTGCTCCAGAAAAACCTGTAAAGAAGCAAAAGACAGGCAAAACTTGGAGAGCTCTGTCATCTTGTAAAC
AGAGCAGCAGCAGCAGAGACGATAACAAGTTTCAGAGTGGGAAAATGAGGTACGTTGGCGTTCGAGATTTTAAAGGCAAA
GTGCTAATTGATATTAGAGAATATTGGATGGATCCTGAAGGTGAAACGAAACCAGGAAGAAAAGGTATTTCTTTAAATCC
AGAACAATGGAGCCAGCTGACGGAACAGATTTCTGACATTGATGATGCAGTAAGAAAACTG

ORF - retro_pabe_1371 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPKSKELVSSSSSGSDSDSEVDKKLKRKKQVAPEKPVKKQKTGETSRALSSSKQSSSSRDDNMFQIGKMR
MPKSKELVSSSSSGSD.DSEVDKKLKRKKQVAPEKPVKKQKTG.T.RALSS.KQSSSSRDDN.FQ.GKMR
RetrocopyMPKSKELVSSSSSGSDPDSEVDKKLKRKKQVAPEKPVKKQKTGKTWRALSSCKQSSSSRDDNKFQSGKMR
ParentalYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQWSQLKEQISDIDDAVRKL
YV.VRDFKGKVLIDIREYWMDPEGE.KPGRKGISLNPEQWSQL.EQISDIDDAVRKL
RetrocopyYVGVRDFKGKVLIDIREYWMDPEGETKPGRKGISLNPEQWSQLTEQISDIDDAVRKL

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
SRP007412_brain_prefrontal_cortex 0 .33 RPM 61 .21 RPM
SRP007412_cerebellum 0 .36 RPM 35 .87 RPM
SRP007412_heart 0 .24 RPM 29 .53 RPM
SRP007412_kidney 0 .43 RPM 30 .83 RPM
SRP007412_liver 0 .34 RPM 25 .74 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_1371 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_1371 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1371 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1662
Gorilla gorilla retro_ggor_1254
Parental genes homology:
Parental genes homology involve 25 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000062382 retrocopies
retro_amel_1331, retro_amel_794,
Canis familiaris ENSCAFG000000188795 retrocopies
retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Callithrix jacchus ENSCJAG000000187182 retrocopies
retro_cjac_1908, retro_cjac_484,
Cavia porcellus ENSCPOG000000055844 retrocopies
retro_cpor_1114, retro_cpor_1481, retro_cpor_834, retro_cpor_854,
Dasypus novemcinctus ENSDNOG000000076115 retrocopies
retro_dnov_1230, retro_dnov_161, retro_dnov_1822, retro_dnov_2156, retro_dnov_400,
Dipodomys ordii ENSDORG000000139162 retrocopies
retro_dord_85, retro_dord_98,
Felis catus ENSFCAG000000060122 retrocopies
retro_fcat_1052, retro_fcat_1313,
Homo sapiens ENSG000001133872 retrocopies
retro_hsap_1662, retro_hsap_3934,
Gorilla gorilla ENSGGOG000000270333 retrocopies
retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana ENSLAFG000000110061 retrocopy
retro_lafr_19,
Macropus eugenii ENSMEUG000000077704 retrocopies
retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus ENSMICG000000145352 retrocopies
retro_mmur_1115, retro_mmur_17,
Myotis lucifugus ENSMLUG000000136856 retrocopies
retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Macaca mulatta ENSMMUG000000114702 retrocopies
retro_mmul_2318, retro_mmul_993,
Monodelphis domestica ENSMODG000000204103 retrocopies
retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furoENSMPUG000000151852 retrocopies
retro_mputfur_186, retro_mputfur_295,
Mus musculus ENSMUSG000000222054 retrocopies
retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus ENSOCUG000000062625 retrocopies
retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii ENSOGAG000000090126 retrocopies
retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Ochotona princeps ENSOPRG000000128872 retrocopies
retro_opri_495, retro_opri_941,
Pongo abelii ENSPPYG00000015379 2 retrocopies
retro_pabe_124, retro_pabe_1371 ,
Rattus norvegicus ENSRNOG0000005056312 retrocopies
retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii ENSSHAG000000149861 retrocopy
retro_shar_628,
Ictidomys tridecemlineatus ENSSTOG000000193642 retrocopies
retro_itri_570, retro_itri_571,
Tarsius syrichta ENSTSYG000000140692 retrocopies
retro_tsyr_528, retro_tsyr_895,


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