RetrogeneDB ID:

retro_pabe_909

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:19658397..19658775(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HINT1
Ensembl ID:ENSPPYG00000015747
Aliases:None
Description:histidine triad nucleotide-binding protein 1 [Source:RefSeq peptide;Acc:NP_001124701]


Retrocopy-Parental alignment summary:






>retro_pabe_909
ATGGCAGATGAGATTGCCAAGGCTCAGGTCGCTCGGCCTGGTGGCGACACGATCTTCGGGAAGATCATCCGCAAGGAAAT
ACCAGCCAAAATCATTTTTGAGGATGACCAGTGCCTTGCTTTCCATGACATTTCCCCTCAAGCACCAACACATTTTCTGG
TGATACCCAAGAAACATATATCCCAGATTTCTGCGGCAGAAGATGATGATGAAAGTCTTCTTGGACACTTAATGATTGTT
GGCAAGAAATGTGCTGCTGATCTGGGCCTGAATAAGGGTTATTGAATGGTAGTGAATGAAGGTTCAGATGGTGGACAGTC
TGTCTACCATGTTCATCTCCATGTTCTTGGAGGTCGGCAGATGCATTGGCCTCCTGGT

ORF - retro_pabe_909 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.41 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADEIAKAQVARPGGDTIFGKIIRKEIPAKIIFEDDRCLAFHDISPQAPTHFLVIPKKHISQISAAEDDD
MADEIAKAQVARPGGDTIFGKIIRKEIPAKIIFEDD.CLAFHDISPQAPTHFLVIPKKHISQISAAEDDD
RetrocopyMADEIAKAQVARPGGDTIFGKIIRKEIPAKIIFEDDQCLAFHDISPQAPTHFLVIPKKHISQISAAEDDD
ParentalESLLGHLMIVGKKCAADLGLNKGYRMVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG
ESLLGHLMIVGKKCAADLGLNKGY.MVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG
RetrocopyESLLGHLMIVGKKCAADLGLNKGY*MVVNEGSDGGQSVYHVHLHVLGGRQMHWPPG

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 .11 RPM 89 .46 RPM
SRP007412_cerebellum 0 .24 RPM 71 .50 RPM
SRP007412_heart 0 .69 RPM 51 .42 RPM
SRP007412_kidney 1 .59 RPM 65 .56 RPM
SRP007412_liver 1 .84 RPM 75 .25 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_909 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_909 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_909 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000321521 retrocopy
Callithrix jacchus ENSCJAG000000143983 retrocopies
Equus caballus ENSECAG000000231803 retrocopies
Erinaceus europaeus ENSEEUG000000081751 retrocopy
Echinops telfairi ENSETEG000000101271 retrocopy
Homo sapiens ENSG000001695671 retrocopy
Gorilla gorilla ENSGGOG000000119671 retrocopy
Macropus eugenii ENSMEUG000000053682 retrocopies
Myotis lucifugus ENSMLUG000000010912 retrocopies
Macaca mulatta ENSMMUG000000099852 retrocopies
Monodelphis domestica ENSMODG000000287273 retrocopies
Mustela putorius furoENSMPUG000000116394 retrocopies
Mus musculus ENSMUSG000000202671 retrocopy
Nomascus leucogenys ENSNLEG000000124311 retrocopy
Oryctolagus cuniculus ENSOCUG000000066075 retrocopies
Otolemur garnettii ENSOGAG000000088502 retrocopies
Procavia capensis ENSPCAG000000047371 retrocopy
Pongo abelii ENSPPYG00000015747 2 retrocopies
retro_pabe_3189, retro_pabe_909 ,
Pongo abelii ENSPPYG000000190821 retrocopy
Pan troglodytes ENSPTRG000000172061 retrocopy
Rattus norvegicus ENSRNOG000000006221 retrocopy
Sarcophilus harrisii ENSSHAG000000058342 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000279204 retrocopies



Copyright © RetrogeneDB 2014-2017