RetrogeneDB ID:

retro_ptro_2436

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:64727268..64727807(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TMEM98
Ensembl ID:ENSPTRG00000008993
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_2436
AAGGCCACAGTGATTGTTGCCATAAGCGTGCTGGCTACCATCTTTCTGGCTTTGTTTGCAGTCTTGGTGGTGGTTTGAGT
GCAGCGCTACCGCTGGCCAGGAGACCTGCTGCAGCGCTATGATTCCAAGCCCATTATGAGTCTCTTGGGTGCCATGGAGA
CCCAATCTGAGCTCTCTGAGTTAGAACTAGATGATGTCATCATCGCCCACTCTGGCATAGAGCCCATTCTGGAGAATGAA
GACTGGATCTAGGATGCCTTGGGTCTCATGTCCCACTGCATTGTCATCTTGAAGATTTGTCACACTTTGAGAGAAAAACT
TGTTGCCATGACAACGGGCTCAGAGGCTGAGAAGAAGACTTCAGCCACTGTCAGCAGCATCATTGTGGTGGCCAAGTGGA
TCATCCCCAGAGTAGATGATGTTGTGAAATCAGTGTACCATCTGTTAAGCACCAAGCTCCTGGATGTGAGTACGACTGCC
CTGCTCCTGTCAGTCATCAGGTGCTGGTAACCAGAAATGCCTGCCATCTGAACAGGGGC

ORF - retro_ptro_2436 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.08 %
Parental protein coverage: 80.09 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalETVVIVAIGVLATIFLASFAALVLVCRQRYCRPRDLLQRYDSKPIVDLIGAMETQSEPSELELDDVVITN
...VIVAI.VLATIFLA.FA.LV.V..QRY..P.DLLQRYDSKPI..L.GAMETQSE.SELELDDV.I..
RetrocopyKATVIVAISVLATIFLALFAVLVVV*VQRYRWPGDLLQRYDSKPIMSLLGAMETQSELSELELDDVIIAH
ParentalPHIEAILENEDWIEDASGLMSHCIAILKICHTLTEKLVAMTMGSGAKMKTSASVSDIIVVAKRISPRVDD
..IE.ILENEDWI.DA.GLMSHCI.ILKICHTL.EKLVAMT.GS.A..KTSA.VS.IIVVAK.I.PRVDD
RetrocopySGIEPILENEDWI*DALGLMSHCIVILKICHTLREKLVAMTTGSEAEKKTSATVSSIIVVAKWIIPRVDD
ParentalVVKSMYPPLDPKLLDARTTALLL-SVSHLVLVTRNACHLTGG
VVKS.Y..L..KLLD...T..LL..VSH.VLVTRNACHL..G
RetrocopyVVKSVYHLLSTKLLDV-STTALL<PVSHQVLVTRNACHLNRG

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 24 .15 RPM
SRP007412_cerebellum 0 .00 RPM 20 .43 RPM
SRP007412_heart 0 .00 RPM 5 .04 RPM
SRP007412_kidney 0 .00 RPM 42 .44 RPM
SRP007412_liver 0 .00 RPM 15 .91 RPM
SRP007412_testis 0 .32 RPM 3 .79 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2436 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2436 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2436 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3605
Pan troglodytes retro_ptro_2990
Gorilla gorilla retro_ggor_2432
Pongo abelii retro_pabe_2961
Macaca mulatta retro_mmul_1835
Callithrix jacchus retro_cjac_2447

Parental genes homology:
Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000145501 retrocopy
Homo sapiens ENSG000000060422 retrocopies
Gorilla gorilla ENSGGOG000000133332 retrocopies
Myotis lucifugus ENSMLUG000000011911 retrocopy
Macaca mulatta ENSMMUG000000223562 retrocopies
Nomascus leucogenys ENSNLEG000000060383 retrocopies
Pongo abelii ENSPPYG000000081662 retrocopies
Pan troglodytes ENSPTRG00000008993 3 retrocopies
retro_ptro_2436 , retro_ptro_2990, retro_ptro_971,



Copyright © RetrogeneDB 2014-2017