RetrogeneDB ID:

retro_ptro_1010

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:15:42200730..42201168(+)
Located in intron of:ENSPTRG00000007025
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAB
Ensembl ID:ENSPTRG00000013529
Aliases:None
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]


Retrocopy-Parental alignment summary:






>retro_ptro_1010
ATACTGTCTCTTTTGGAAAAGTTCTTGATCCCTAGTGCTTCACAAGCAGAGAGCAAAGTCTTCTATTTGAAAATGAAAGG
CAATTACTACTGTTACTTGGCTGAGGTTGCCACTTATGATGACAAGTAAGGGATTGTCGATCAGTCACAACAAGCATACC
AAGAAGCCTTTGAAACCAGCAAAAAGGAAATACATCCAACACATCCTATCAGACTGGGTCTGGCCCTTAACTTCTCTGTG
TTCTCTTATGAGATTCTGAACTCCCCAGAGAAAGCCTGCTGTCTTCCAAAGACAGCTTTTGATGGAGCCATTGCTGAACT
TGATACATTAAGGGAAGAGTCATACAAAGACAGCACACTAATAATGCAATTACTGAGAGACAACTTGACGTTGTGGACAT
CAGATACCTAAGGAGACAAAGCTGAAGCAGGAGAAGGA

ORF - retro_ptro_1010 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.4 %
Parental protein coverage: 59.35 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPI
.L.LL.K.LIP.A.Q.ESKVFYLKMKG.Y..YL.EVA..D.K...V..SQQAYQEAFE.SKKE..PTHPI
RetrocopyILSLLEKFLIPSASQAESKVFYLKMKGNYYCYLAEVATYDDK*GIVDQSQQAYQEAFETSKKEIHPTHPI
ParentalRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDE
RLGLALNFSVF.YEILNSPEKAC.L.KTAFD.AIAELDTL.EESYKDSTLIMQLLRDNLTLWTS...GD.
RetrocopyRLGLALNFSVFSYEILNSPEKACCLPKTAFDGAIAELDTLREESYKDSTLIMQLLRDNLTLWTSDT*GDK
ParentalGDAGEG
..AGEG
RetrocopyAEAGEG

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 .02 RPM 344 .89 RPM
SRP007412_cerebellum 0 .00 RPM 282 .74 RPM
SRP007412_heart 0 .00 RPM 140 .57 RPM
SRP007412_kidney 0 .03 RPM 222 .42 RPM
SRP007412_liver 0 .03 RPM 119 .81 RPM
SRP007412_testis 0 .32 RPM 83 .89 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1010 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1010 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1010 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 27 parental genes, and 146 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000117961 retrocopy
Choloepus hoffmanni ENSCHOG0000000578215 retrocopies
Callithrix jacchus ENSCJAG000000176642 retrocopies
Dipodomys ordii ENSDORG0000000106414 retrocopies
Echinops telfairi ENSETEG000000099674 retrocopies
Homo sapiens ENSG000001669134 retrocopies
Gorilla gorilla ENSGGOG000000045802 retrocopies
Microcebus murinus ENSMICG000000009737 retrocopies
Myotis lucifugus ENSMLUG000000063191 retrocopy
Macaca mulatta ENSMMUG000000132063 retrocopies
Monodelphis domestica ENSMODG000000162002 retrocopies
Nomascus leucogenys ENSNLEG000000066432 retrocopies
Oryctolagus cuniculus ENSOCUG000000030021 retrocopy
Otolemur garnettii ENSOGAG000000089093 retrocopies
Ochotona princeps ENSOPRG000000118362 retrocopies
Pongo abelii ENSPPYG000000110415 retrocopies
Pan troglodytes ENSPTRG000000085215 retrocopies
Pan troglodytes ENSPTRG000000116412 retrocopies
Pan troglodytes ENSPTRG00000013529 12 retrocopies
Pteropus vampyrus ENSPVAG000000126621 retrocopy
Sarcophilus harrisii ENSSHAG000000112411 retrocopy
Sus scrofa ENSSSCG000000073811 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000037331 retrocopy
Tupaia belangeri ENSTBEG0000000280647 retrocopies
Tarsius syrichta ENSTSYG000000065374 retrocopies
Tursiops truncatus ENSTTRG000000076151 retrocopy
Vicugna pacos ENSVPAG000000050233 retrocopies



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