RetrogeneDB ID:

retro_ptro_1999

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:4:83017990..83018435(+)
Located in intron of:ENSPTRG00000016049
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TPI1
Ensembl ID:ENSPTRG00000004595
Aliases:None
Description:Pan troglodytes triosephosphate isomerase 1 (TPI1), mRNA. [Source:RefSeq mRNA;Acc:NM_001071782]


Retrocopy-Parental alignment summary:






>retro_ptro_1999
GGGAACTGGAAGATGAATGGGTGGAAGAAGAGTCTTGGGGAGCTCATTGACACTGAACGTGACCAAGGTGCCAGCCGACG
CTGAGGTGGTTTTCTCTCCCCCAACTGCCTATATCGACTTCACCCAGCAGAAGCTAGATCCCAAGATTGCTGTGCCTGTG
CAGAACTGCTACAAAGTGACTAATGGGGCCTTTACTGGGGAGATCAGCCCTGGCATAATCAAAGACTGCGGAGGTACGTG
GGTGGTCCTGGGGCACTCAGAGAGAAGGCATGTCTTTGGGGAGTCAGATGAACTGATTGAGCAGAAAGTGGCCCATGCTC
TGGCAGAGGGACTTGGAGTAATCACCTGCATTGGGAAGAAGCTAGATGCAAGGGAAGCTGGCATCACTGAGAAGGTTGTT
TTCGAGCAGGCAAAGGTCATCACAGATAAGGTGAAGGGACTAAGC

ORF - retro_ptro_1999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82. %
Parental protein coverage: 59.84 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGNWKMNGRKQS-LGELIGTLNAAKVPADTEVVCAPPTAYIDFARQKLDPKIAVAAQNCYKVTNGAFTGEI
GNWKMNG.K.S.LG....TLN..KVPAD.EVV..PPTAYIDF..QKLDPKIAV..QNCYKVTNGAFTGEI
RetrocopyGNWKMNGWKKS>LGSSL-TLNVTKVPADAEVVFSPPTAYIDFTQQKLDPKIAVPVQNCYKVTNGAFTGEI
ParentalSPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACIGEKLDEREAGITEKVVFEQTK
SPG.IKDCG.TWVVLGHSERRHVFGESDELI.QKVAHALAEGLGVI.CIG.KLD.REAGITEKVVFEQ.K
RetrocopySPGIIKDCGGTWVVLGHSERRHVFGESDELIEQKVAHALAEGLGVITCIGKKLDAREAGITEKVVFEQAK
ParentalVIADNVKDWS
VI.D.VK..S
RetrocopyVITDKVKGLS

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 602 .46 RPM
SRP007412_cerebellum 0 .00 RPM 278 .72 RPM
SRP007412_heart 0 .00 RPM 265 .67 RPM
SRP007412_kidney 0 .00 RPM 371 .36 RPM
SRP007412_liver 0 .00 RPM 210 .35 RPM
SRP007412_testis 0 .00 RPM 142 .16 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1999 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1999 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1999 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3038
Callithrix jacchus retro_cjac_2190

Parental genes homology:
Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000073482 retrocopies
Homo sapiens ENSG000001116693 retrocopies
Gorilla gorilla ENSGGOG000000026231 retrocopy
Macropus eugenii ENSMEUG000000069775 retrocopies
Myotis lucifugus ENSMLUG000000249894 retrocopies
Macaca mulatta ENSMMUG000000051942 retrocopies
Mustela putorius furoENSMPUG000000167741 retrocopy
Mus musculus ENSMUSG000000234564 retrocopies
Nomascus leucogenys ENSNLEG000000048212 retrocopies
Otolemur garnettii ENSOGAG000000312541 retrocopy
Pan troglodytes ENSPTRG00000004595 4 retrocopies
Rattus norvegicus ENSRNOG000000152901 retrocopy
Rattus norvegicus ENSRNOG000000506692 retrocopies



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