RetrogeneDB ID:

retro_pabe_1828

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:20:45503515..45503810(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SRM
Ensembl ID:ENSPPYG00000001892
Aliases:None
Description:spermidine synthase [Source:HGNC Symbol;Acc:11296]


Retrocopy-Parental alignment summary:






>retro_pabe_1828
GATGTCATCCAAGTCTCTAGGAAGTTCCTGCCAGGCATGGCCAGTTGCTACTCTAGTTCAAAGCTGACCCTTCATGTGGA
TGACGTTTTGAGTTCATGAAGCAGAACTAGGATGTCTTCGATGTTATCACTGACTTCCCAGACCACATGGGCCCGGCTGA
AAGCCTCTTCAAGGAAGCCTATTGTCAGCGGATGAAGGTGAAGATGGCCCTCGAGGAGGATGGCATTCTCTGCTGCCAGG
GAGAGCGCCAGTGGCTGCACCTTCACCTCATAAGGAGATGCGGCAGTTCTGCCAG

ORF - retro_pabe_1828 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.45 %
Parental protein coverage: 56. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalDVIQVSKKFLPGMAIGYSSSKLTLHVGD-GFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQLMKT-
DVIQVS.KFLPGMA..YSSSKLTLHV.D..FEFMKQN.D.FDV.ITD..D.MGPAESLFKE.Y.Q.MK..
RetrocopyDVIQVSRKFLPGMASCYSSSKLTLHVDD<RFEFMKQN*DVFDV-ITDFPDHMGPAESLFKEAYCQRMKVK
Parental-ALKEDGVLCCQGECQWLHLDLI-KEMRQFCQ
.AL.EDG.LCCQGE.QWLHL.LI.KEMRQFCQ
RetrocopyMALEEDGILCCQGERQWLHLHLI<KEMRQFCQ

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 38 .26 RPM
SRP007412_cerebellum 0 .00 RPM 6 .69 RPM
SRP007412_heart 0 .00 RPM 6 .41 RPM
SRP007412_kidney 0 .03 RPM 16 .18 RPM
SRP007412_liver 0 .00 RPM 15 .42 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1828 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1828 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1828 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 20 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000023544 retrocopies
Homo sapiens ENSG000001166492 retrocopies
Gorilla gorilla ENSGGOG000000143851 retrocopy
Macropus eugenii ENSMEUG000000070022 retrocopies
Macaca mulatta ENSMMUG000000193212 retrocopies
Nomascus leucogenys ENSNLEG000000095323 retrocopies
Pongo abelii ENSPPYG00000001892 3 retrocopies
retro_pabe_1181, retro_pabe_1828 , retro_pabe_2044,
Pan troglodytes ENSPTRG000000001383 retrocopies



Copyright © RetrogeneDB 2014-2017