RetrogeneDB ID:

retro_pabe_1549

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:18:19872833..19873180(+)
Located in intron of:ENSPPYG00000008993
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SDHD
Ensembl ID:ENSPPYG00000003876
Aliases:None
Description:Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q5RC29]


Retrocopy-Parental alignment summary:






>retro_pabe_1549
ATGGCGGTTCTCTGGAGACTGAGTACCCTTTGCGGTGCCCAAGGAGGCCAAACTCTGTTGCTGCGAACCCCAGTGGTCAG
ACCTGCTCATATCTCAGCATTACTTCAGAACCGACCTACCCCAGAATGGTGTGGAGTGCAGTACATTGGCTTGTCACCGA
GCCACCATTCTGGTTCCCAGGTTGCGTCTCTCCACTGGACTAGTGAGAGGGTCGTCAGTGTTTTGCTCCTGGGCCTGCTT
CCAGCTGCTTATTTGAATCCTTGGCTCTGTGATGGACTCTACTCCTGGCTGCAACCCTCACTCTTCATAGTTACTGGGGC
CTTGAACAAGTTGTTACTATGTTCATG

ORF - retro_pabe_1549 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.49 %
Parental protein coverage: 72.33 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAVLWRLSAVCGAQGGRALLLRTPVVRPAHISAFLQDRPIPEWCGVQHIHLSPGHHSGSKAASLHWTSER
MAVLWRLS..CGAQGG..LLLRTPVVRPAHISA.LQ.RP.PEWCGVQ.I.LSP.HHSGS..ASLHWTSER
RetrocopyMAVLWRLSTLCGAQGGQTLLLRTPVVRPAHISALLQNRPTPEWCGVQYIGLSPSHHSGSQVASLHWTSER
ParentalVVSVLLLGLLPAAYLNPC-SAMDYS-LAATLTLHGHWGLGQVVTDYV
VVSVLLLGLLPAAYLNP..S.MD...LAATLTLH..WGL.QVVT...
RetrocopyVVSVLLLGLLPAAYLNPW>SVMDST>LAATLTLHSYWGLEQVVTMFM

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 .06 RPM 8 .46 RPM
SRP007412_cerebellum 0 .12 RPM 5 .23 RPM
SRP007412_heart 0 .03 RPM 23 .00 RPM
SRP007412_kidney 0 .03 RPM 24 .73 RPM
SRP007412_liver 0 .09 RPM 22 .58 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1549 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1549 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1549 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 8 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000109754 retrocopies
Echinops telfairi ENSETEG000000084241 retrocopy
Homo sapiens ENSG000002043708 retrocopies
Gorilla gorilla ENSGGOG000000264961 retrocopy
Loxodonta africana ENSLAFG000000027631 retrocopy
Macaca mulatta ENSMMUG000000152471 retrocopy
Otolemur garnettii ENSOGAG000000085685 retrocopies
Pongo abelii ENSPPYG00000003876 5 retrocopies



Copyright © RetrogeneDB 2014-2017