RetrogeneDB ID:

retro_pabe_2780

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:127219691..127220083(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C1orf146
Ensembl ID:ENSPPYG00000001156
Aliases:None
Description:chromosome 1 open reading frame 146 [Source:HGNC Symbol;Acc:24032]


Retrocopy-Parental alignment summary:






>retro_pabe_2780
GTTAGTATTAGCTCATTTCTTTAGTGTTATGAAGTTGTAGCTGCCCTAGAAAATTAAAGCCATAAGTTTTGGTAATCAAA
CAAATGGAAAATGGATCAATTATATTTCCTTTTTCTGTAGTTACATTTTAATTGATGGATGCTAAGGAATGCCTATGTTA
GCTGAAGCACTATTTCTAGCAAAATATGAGAAGTTCATAAAATATTCACTGAAATAACTTTTTGAATTTATCTGCTGCCC
TTTATGGACTTGAGAAATGGGAAATGTTGAGTATTCGGCAGAGATTTCTGAGTAGTAATTTACAAATAGTTTCAGTATAA
AACATAGTTAATGTTACTAATCTTGTACACACTATAGCTAAGACCACCCTATATAGAAATATGGATAGCATA

ORF - retro_pabe_2780 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.52 %
Parental protein coverage: 73.33 %
Number of stop codons detected: 5
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIIISSSLKSYEVATALENRSHK-VRYSDSVENGSIIFSLSGVAFLLMDTKECL-LSTEEIFLAKIEKFI-
..ISS.L..YEV..ALEN.SHK.V......ENGSIIF..S.V.F.LMD.KECL....E..FLAK.EKFI.
RetrocopyVSISSFL*CYEVVAALEN*SHK<VLVIKQMENGSIIFPFSVVTF*LMDAKECL<MLAEALFLAKYEKFI>
ParentalNIHQNSFLVLSAALHGPEEWKLMFRIQQRFLGCNLRILPVHNTVNAINLMCTIAKTTSKPYIDSI
NIH.N.FL.LSAAL.G.E.W..M..I.QRFL..NL.I..V.N.VN..NL..TIAKTT.....DSI
RetrocopyNIH*NNFLNLSAALYGLEKWE-MLSIRQRFLSSNLQIVSV*NIVNVTNLVHTIAKTTLYRNMDSI

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 .00 RPM
SRP007412_cerebellum 0 .00 RPM 0 .12 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .03 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2780 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2780 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2780 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3381
Pan troglodytes retro_ptro_2298
Gorilla gorilla retro_ggor_2289
Macaca mulatta retro_mmul_2107
Callithrix jacchus retro_cjac_1817

Parental genes homology:
Parental genes homology involve 14 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000279361 retrocopy
Choloepus hoffmanni ENSCHOG000000040121 retrocopy
Callithrix jacchus ENSCJAG000000175471 retrocopy
Erinaceus europaeus ENSEEUG000000030831 retrocopy
Homo sapiens ENSG000002039101 retrocopy
Gorilla gorilla ENSGGOG000000066531 retrocopy
Macropus eugenii ENSMEUG000000133111 retrocopy
Myotis lucifugus ENSMLUG000000169841 retrocopy
Macaca mulatta ENSMMUG000000100941 retrocopy
Nomascus leucogenys ENSNLEG000000104261 retrocopy
Pongo abelii ENSPPYG00000001156 1 retrocopy
retro_pabe_2780 ,
Pan troglodytes ENSPTRG000000305301 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000125061 retrocopy
Tursiops truncatus ENSTTRG000000144261 retrocopy



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