RetrogeneDB ID:

retro_pabe_1346

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:16:30613216..30613729(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A1
Ensembl ID:ENSPPYG00000029785
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]


Retrocopy-Parental alignment summary:






>retro_pabe_1346
GAGTTCCTCGGCACCCAGATGCGGGATGCCCAGGGACTGCTAAACAGCAGGCGCGGGCTGCTGTGCGGCCTGGGCGCCGG
CGTGGCCGAGGCCGTGGTGGTTGTCCCTCCCATGGAGACCATCAAAGTGAAGTTCATCCACGACCAGACCTCCCCAAACC
CAAGAACAGAGAATTCTTTGGGGTTAGGGAGATTGTGCGGGAACAAGAGCTGAGGGGATTTACCAGGGCCTCACGGCCTC
CACGCTGAAGCAGGGCTGGAACCAGGCCATTGCTTCTTCGTCCTGACCTCCCCGCAGCAACTGATACCAAAGGGACAAAC
CCATGAACCCGCTGATCATTGGGGTCTTCTGAGCCATTGTGGGCGCAGACAGCGTCTTCGGAAACGCCCCTCTGGACAGG
ATCGAGACCCGGATGCGGGGCGTGGAAGTGCACAAACACCGGAACAGTGGAATGCAGCTGCAGATCCCGAGGAAGGAGGG
GCTCAATGCCTTCACAAGGGCACTGCCCCCCGC

ORF - retro_pabe_1346 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.88 %
Parental protein coverage: 85.1 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPH-PKYKGFFHGVREIVRE
EFL...MRDAQG.L.S.RGLLCGLGAGVAEAVVVV.PMETIKVKFIHDQTSP..PK...FF.GVREIVRE
RetrocopyEFLGTQMRDAQGLLNSRRGLLCGLGAGVAEAVVVVPPMETIKVKFIHDQTSPN<PKNREFF-GVREIVRE
ParentalQGLK-GTYQGLTATVLKQGSNQAIR-FFVMTSLR-NWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPL
Q.L..G.YQGLTA..LKQG.NQAI..FFV.TS...N.Y..D...KPMNPLI.GVF.AI.GA.SVFGN.PL
RetrocopyQELR<GIYQGLTASTLKQGWNQAIA<FFVLTSPQ>N*YQRD---KPMNPLIIGVF*AIVGADSVFGNAPL
ParentalDVIKTRMQGLEAHKYRNTWDCGLQILRKEGLKAF-YKGTVPR
D.I.TRM.G.E.HK.RN.....LQI.RKEGL.AF..KGT.PR
RetrocopyDRIETRMRGVEVHKHRNS-GMQLQIPRKEGLNAF<HKGTAPR

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 16 .70 RPM
SRP007412_cerebellum 0 .00 RPM 10 .58 RPM
SRP007412_heart 0 .00 RPM 5 .99 RPM
SRP007412_kidney 0 .00 RPM 187 .78 RPM
SRP007412_liver 0 .00 RPM 61 .54 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1346 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1346 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1346 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001000752 retrocopies
Gorilla gorilla ENSGGOG000000061982 retrocopies
Macaca mulatta ENSMMUG000000054314 retrocopies
Nomascus leucogenys ENSNLEG000000052152 retrocopies
Ochotona princeps ENSOPRG000000116491 retrocopy
Pongo abelii ENSPPYG00000029785 9 retrocopies
Pan troglodytes ENSPTRG000000140573 retrocopies
Tursiops truncatus ENSTTRG000000068451 retrocopy



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