RetrogeneDB ID:

retro_ptro_2626

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:7:56291788..56292276(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:YWHAE
Ensembl ID:ENSPTRG00000008521
Aliases:None
Description:Pan troglodytes tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (YWHAE), mRNA. [Source:RefSeq mRNA;Acc:NM_001246368]


Retrocopy-Parental alignment summary:






>retro_ptro_2626
TTCCAAGAAATAGTGTAGTCAATGAAGAAAGTAGCAGGGATGGATGTGGAGATGACAGTTGAAGAAAAAAACCTCCTATC
TGTTTCATATAACAATGTGATTGAAGCTAGAAGAGCCTTCTGGAGAATAATCAGCATTGAACAGAAAGAAGAAAACAAGG
GAGAAGACAAGCTAAAAATGATTTGGGAATATCAGCAAATGGTTGAGACTGAGCTAAATTTAATCTGTTGTCACTTTCTG
TATGTACTGGACAAAACCTCATTCCAGCAGCTAACACTGGCGAGTCCAAGGTTTTCTATTATAAAATGAAAAGGGACTAC
CACAGGTATCTGGCAGAATTTGCCACAGGAAATGACAGGAAGGAGGCTGTGGAGAACAGCCTAGTGGGTTATAAAGCTGC
TAGTGATATTGCTATGACAGAACTTCCACCTGCGCATCCTATTCGCTTAAGTCTTGCTCTCAATTTTTCCTTATTCTACT
ACGAAATT

ORF - retro_ptro_2626 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.34 %
Parental protein coverage: 64.71 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalYDEMVESMKKVAGMDVELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKGGEDKLKMIREYRQMV
..E.V.SMKKVAGMDVE.TVEE.NLLSV.Y.NVI.ARRA.WRIIS.IEQKEENKG.EDKLKMI.EY.QMV
RetrocopyFQEIV*SMKKVAGMDVEMTVEEKNLLSVSYNNVIEARRAFWRIIS-IEQKEENKG-EDKLKMIWEYQQMV
ParentalETELKLICCDILDVLDK-HLIPAANTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAENSLVAYKAASDI
ETEL.LICC..L.VLDK..LIPAANTGESKVFYYKMK.DYHRYLAEFATGNDRKEA.ENSLV.YKAASDI
RetrocopyETELNLICCHFLYVLDK<NLIPAANTGESKVFYYKMKRDYHRYLAEFATGNDRKEAVENSLVGYKAASDI
ParentalAMTELPPTHPIRLGLALNFSVFYYEI
AMTELPP.HPIRL.LALNFS.FYYEI
RetrocopyAMTELPPAHPIRLSLALNFSLFYYEI

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 546 .12 RPM
SRP007412_cerebellum 0 .04 RPM 571 .39 RPM
SRP007412_heart 0 .03 RPM 404 .14 RPM
SRP007412_kidney 0 .05 RPM 351 .38 RPM
SRP007412_liver 0 .00 RPM 235 .52 RPM
SRP007412_testis 0 .63 RPM 787 .74 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2626 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2626 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2626 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3851
Pan troglodytes retro_ptro_2624
Pan troglodytes retro_ptro_2993
Gorilla gorilla retro_ggor_2596

Parental genes homology:
Parental genes homology involve 16 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000056643 retrocopies
Choloepus hoffmanni ENSCHOG000000108612 retrocopies
Ciona intestinalis ENSCING000000238561 retrocopy
Ciona savignyi ENSCSAVG000000117232 retrocopies
Echinops telfairi ENSETEG000000120562 retrocopies
Homo sapiens ENSG000001089534 retrocopies
Gorilla gorilla ENSGGOG000000168401 retrocopy
Monodelphis domestica ENSMODG000000101742 retrocopies
Nomascus leucogenys ENSNLEG000000006562 retrocopies
Otolemur garnettii ENSOGAG000000061552 retrocopies
Pongo abelii ENSPPYG000000077694 retrocopies
Pan troglodytes ENSPTRG00000008521 5 retrocopies
Pan troglodytes ENSPTRG000000116412 retrocopies
Pan troglodytes ENSPTRG0000001352912 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000050841 retrocopy
Vicugna pacos ENSVPAG000000102883 retrocopies



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