RetrogeneDB ID:

retro_pabe_1565

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:18:63245079..63245382(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17-C18orf32
Ensembl ID:ENSPPYG00000009151
Aliases:None
Description:RPL17-C18orf32 readthrough [Source:HGNC Symbol;Acc:44661]


Retrocopy-Parental alignment summary:






>retro_pabe_1565
ATCTTTATGTTCGCTTTAAGAACACCCACGTAACTGTGCAGGCCATCAAGGTATGCATACCCAAAAAACCACCAAGTACC
TGAAAGATGTTACTTTTCAGAGGCACTGTGTGCCTTTCCATCATTACAAAGGTGGAGCTGGCATGTGTGCCCAGGCCAAA
CAATGGGGCTGGACGCAGGGTTGGTGGCCCGAAAATGTGTTGAATTTTTGCTGCATGTGCTTAAAAATGCAGAGAGCAAT
GCTGAACTTCAGGGTTTAGATGTAGATTCTTGGATCATTGAGCACATTCAGTTGAGCAAAGCC

ORF - retro_pabe_1565 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.38 %
Parental protein coverage: 77.86 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIFVFTLR-NTRETAQAIK-GMHIRKATKYLKDVTLQKQCVPFRRYNGGVGRCAQAKQWGWTQGRWP-KKS
IF.F.LR.NT..T.QAIK.GMH..K.TKYLKDVT.Q..CVPF..Y.GG.G.CAQAKQWGWTQG.WP..K.
RetrocopyIFMFALR<NTHVTVQAIK<GMHTQKTTKYLKDVTFQRHCVPFHHYKGGAGMCAQAKQWGWTQGWWP<RKC
ParentalAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNKA
.EFLLH.LKNAESNAEL.GLDVDS..IEHIQ..KA
RetrocopyVEFLLHVLKNAESNAELQGLDVDSWIIEHIQLSKA

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






(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 .00 RPM 0 .22 RPM
SRP007412_cerebellum 0 .00 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .09 RPM
SRP007412_kidney 0 .13 RPM 0 .07 RPM
SRP007412_liver 0 .00 RPM 0 .09 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1565 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1565 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1565 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1267
Equus caballus retro_ecab_977

Parental genes homology:
Parental genes homology involve 32 parental genes, and 803 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
Bos taurus ENSBTAG000000229025 retrocopies
Canis familiaris ENSCAFG000000190447 retrocopies
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Callithrix jacchus ENSCJAG000000047794 retrocopies
Cavia porcellus ENSCPOG0000001933731 retrocopies
Equus caballus ENSECAG000000115479 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Felis catus ENSFCAG0000001134243 retrocopies
Homo sapiens ENSG0000026568133 retrocopies
Gorilla gorilla ENSGGOG000000266971 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Loxodonta africana ENSLAFG0000000556916 retrocopies
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Monodelphis domestica ENSMODG0000000353411 retrocopies
Mustela putorius furoENSMPUG000000008017 retrocopies
Mus musculus ENSMUSG0000006232880 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG00000009151 43 retrocopies
Pan troglodytes ENSPTRG0000001001251 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Rattus norvegicus ENSRNOG0000001868048 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Sus scrofa ENSSSCG0000002964230 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000000519333 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



Copyright © RetrogeneDB 2014-2017