RetrogeneDB ID:

retro_mmus_2471

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:70248638..70249442(-)
Located in intron of:ENSMUSG00000039298
Retrocopy
information
Ensembl ID:ENSMUSG00000080902
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ywhaq
Ensembl ID:ENSMUSG00000076432
Aliases:Ywhaq, 2700028P07Rik, AA409740, AU021156, R74690
Description:tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide [Source:MGI Symbol;Acc:MGI:891963]


Retrocopy-Parental alignment summary:






>retro_mmus_2471
ACTCGCGTCGCGGCTGCGGAGACTAGAAGGAGGACTCCGGATCCGGCTCGGCGCTCGCCCTCGCTCGCCATGGAGAAGAC
CGAGCTGATCCAGAAGGCCAAGCTGGCCGAGCAGGCCGAGCGCTACGACGACATGGCCACCTGCATGAAAGCCGTGACGG
AGCAGGGCGCCGAGCTGTCCAACGAGGAGCGCAACCTGCTGTCGGTGGCCTACAAAAACGTGGTAGGGGGCCGCAGGTCC
GCCTGGAGGGTCATCTCGAGCATTGAGCAGAAGACCGACACCTCTGACAAGAAGTTGCAGCTGATCAAGGACTATCGGGA
GAAAGTGGAGTCGGAGCTGAGGTCCATCTGCACCACGGTCCTGGAATTGTTGGATAAGTATTTAATAGCCAATGCAACTA
ATCCAGAGAGTAAGGTCTTCTATCTGAAAATGAAGGGAGATTATTTCCGGTATCTTGCTGAAGTAGCTTGTGGTGATGAT
CGAAAACAAACAATAGAAAATTCCCAAGGAGCCTACCAAGAGGCGTTTGATATAAGCAAGAAGGAGATGCAGCCTACGCA
TCCAATCCGCCTGGGGCTGGCTCTTAACTTTTCTGTATTTTACTATGAGATCCTTAATAATCCAGAGCTTGCCTGCACAC
TGGCTAAAACGGCTTTTGATGAGGCCATCGCAGAGCTCGATACACTGAACGAAGACTCCTACAAAGACAGCACCCTCATC
ATGCAGTTGCTTAGAGACAACTTAACATTATGGACATCAGACAGTGCAGGAGAAGAATGTGATGCAGCAGAGGGGGCTGA
AAAC

ORF - retro_mmus_2471 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.27 %
Parental protein coverage: 88.45 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTRVAAAETRRRTPDPARRSPSLAMEKTELIQKAKLAEQAERYDDMATCMKAVTEQGAELSNEERNLLSVA
TRVAAAETRRRTPDPARRSPSLAMEKTELIQ..........YDDMATCMKAVTEQGAELSNEERNLLSVA
RetrocopyTRVAAAETRRRTPDPARRSPSLAMEKTELIQXXXXXXXXXXYDDMATCMKAVTEQGAELSNEERNLLSVA
ParentalYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVF
YKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVF
RetrocopyYKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVF
ParentalYLKMKGDYFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPEL
YLKMKGDYFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPEL
RetrocopyYLKMKGDYFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPEL
ParentalACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN
ACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN
RetrocopyACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEECDAAEGAEN

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 0 .02 RPM 71 .61 RPM
SRP007412_cerebellum 0 .13 RPM 42 .60 RPM
SRP007412_heart 0 .06 RPM 9 .62 RPM
SRP007412_kidney 0 .10 RPM 23 .25 RPM
SRP007412_liver 0 .03 RPM 10 .16 RPM
SRP007412_testis 0 .09 RPM 33 .98 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2471 was not detected
No EST(s) were mapped for retro_mmus_2471 retrocopy.


TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_10634496 libraries73 libraries643 libraries192 libraries68 libraries

The graphical summary, for retro_mmus_2471 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

retro_mmus_2471 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2471 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000049251 retrocopy
Echinops telfairi ENSETEG000000153594 retrocopies
Felis catus ENSFCAG000000078542 retrocopies
Myotis lucifugus ENSMLUG000000053831 retrocopy
Monodelphis domestica ENSMODG000000147401 retrocopy
Mus musculus ENSMUSG000000222853 retrocopies
Mus musculus ENSMUSG00000076432 10 retrocopies
Nomascus leucogenys ENSNLEG000000135343 retrocopies
Oryctolagus cuniculus ENSOCUG000000104821 retrocopy
Otolemur garnettii ENSOGAG000000005473 retrocopies
Rattus norvegicus ENSRNOG000000081045 retrocopies
Sorex araneus ENSSARG000000124764 retrocopies
Tursiops truncatus ENSTTRG000000008714 retrocopies



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