RetrogeneDB ID:

retro_ptro_1486

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:22:23209156..23209438(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARL5A
Ensembl ID:ENSPTRG00000012538
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_1486
ATGAGAATTTTCTTCCCCAGAACGTGGAGACTGTTCGATCACCAGGAGCACAAAGTTATCATTGTTGGGCTGGATAATGC
AGGGAAAACTACCATTCTTTACCAGTTTTCTATGAATGAGGTTGTACATACATCTCCTATAATAGGAAGTAATGTAGAAG
AGATAGTGATTAATAATACGCGTTTCCTAATGTGGGATATTGGTGGCCAAGAATCTTTTCGTTCTTCCTGGAACACTTAC
TGTACTAACACAGAGTTGATAATAGTTGTGGACAGTACAGAC

ORF - retro_ptro_1486 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.42 %
Parental protein coverage: 53.07 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGILFTRIWRLFNHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPTIGSNVEEIVINNTRFLMWDIGGQ
M.I.F.R.WRLF.HQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSP.IGSNVEEIVINNTRFLMWDIGGQ
RetrocopyMRIFFPRTWRLFDHQEHKVIIVGLDNAGKTTILYQFSMNEVVHTSPIIGSNVEEIVINNTRFLMWDIGGQ
ParentalESLRSSWNTYYTNTEFVIVVVDSTD
ES.RSSWNTY.TNTE..I.VVDSTD
RetrocopyESFRSSWNTYCTNTE-LIIVVDSTD

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 10 .40 RPM
SRP007412_cerebellum 0 .04 RPM 16 .81 RPM
SRP007412_heart 0 .06 RPM 20 .72 RPM
SRP007412_kidney 0 .00 RPM 21 .55 RPM
SRP007412_liver 0 .00 RPM 7 .17 RPM
SRP007412_testis 0 .11 RPM 8 .01 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1486 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1486 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1486 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2549
Gorilla gorilla retro_ggor_1594

Parental genes homology:
Parental genes homology involve 17 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000506225 retrocopies
Callithrix jacchus ENSCJAG000000033119 retrocopies
Cavia porcellus ENSCPOG000000052091 retrocopy
Dasypus novemcinctus ENSDNOG0000001333116 retrocopies
Felis catus ENSFCAG000000147422 retrocopies
Homo sapiens ENSG000001629805 retrocopies
Loxodonta africana ENSLAFG000000321044 retrocopies
Microcebus murinus ENSMICG000000157887 retrocopies
Macaca mulatta ENSMMUG000000105215 retrocopies
Monodelphis domestica ENSMODG000000039781 retrocopy
Mus musculus ENSMUSG000000360931 retrocopy
Nomascus leucogenys ENSNLEG000000111912 retrocopies
Otolemur garnettii ENSOGAG000000114246 retrocopies
Pongo abelii ENSPPYG000000128484 retrocopies
Pan troglodytes ENSPTRG00000012538 5 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000163261 retrocopy
Tupaia belangeri ENSTBEG000000115118 retrocopies



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