RetrogeneDB ID:

retro_mmus_2250

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:48026014..48026605(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
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_2250
CGGGGTGTGTGGGGGGGGGGTAGGTCCTCCTGGAGGGTCATCTTGAACATTGAGCAGAAGACCGACACCTCCGACAAGAA
GTTGCAGCTGATCAAGGACTATTGGGAGAAAGTGGAGTCGGAGCTGAGGTCCATCTGCACCATGGGCCTGGAATTGTTGG
ATAAGTATTTAATAGCCAGTGCAACTAATCCCGAGAATAAGGTCTTCTATCTGAAAATAAAGGGAGATTATTTCCAATAT
CTTGCTGAAGTAGCTTGTGGTGACGATCAAAAAGAAACAATAAAAAATTCCCAAGGAGCCTACCAAAAGGCTTTTGATAT
AAGCAAGAAAGAGATGCAGCCTTCGCATCCAATCCACCTGGTGTTGGCTCTTAACTTTTCTGTATTTTACTATGAGATCC
TAATAATCCAGAGCTTGCCTGCACACTGGCTAAAATGGCTTTTGACGAGGCCATCGCAGAGCTTGATACACTGAACGAAG
ACTCCTACAAAGACAGCACCCTCATCATGCAGTTGCTTAGAGACAACTTAACATTAATGGACATCGAACAGTGCAGGAGA
AGAATGTGATGCAGCAGAGGGGGCCGAAAAC

ORF - retro_mmus_2250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.43 %
Parental protein coverage: 80.41 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKNVVGGRRSAWRVISSIEQKTDTSDKKLQLIKDYREKVESELRSICTTVLELLDKYLIANATNPESKVFY
..V....RS.WRVI..IEQKTDTSDKKLQLIKDY.EKVESELRSICT..LELLDKYLIA.ATNPE.KVFY
RetrocopyRGVXXXXRSSWRVILNIEQKTDTSDKKLQLIKDYWEKVESELRSICTMGLELLDKYLIASATNPENKVFY
ParentalLKMKGDYFRYLAEVACGDDRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEIL-NNPEL
LK.KGDYF.YLAEVACGDD.K.TI.NSQGAYQ.AFDISKKEMQP.HPI.L.LALNFSVFYYEIL.NNPEL
RetrocopyLKIKGDYFQYLAEVACGDDQKETIKNSQGAYQKAFDISKKEMQPSHPIHLVLALNFSVFYYEIL<NNPEL
ParentalACTLAKTAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTL-WTSDSAGEECDAAEGAEN
ACTLAK.AFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTL.WTS.SAGEECDAAEGAEN
RetrocopyACTLAKMAFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTL>WTSNSAGEECDAAEGAEN

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 .00 RPM 42 .60 RPM
SRP007412_heart 0 .00 RPM 9 .62 RPM
SRP007412_kidney 0 .00 RPM 23 .25 RPM
SRP007412_liver 0 .00 RPM 10 .16 RPM
SRP007412_testis 0 .00 RPM 33 .98 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2250 was not detected
No EST(s) were mapped for retro_mmus_2250 retrocopy.
No TSS is located nearby retro_mmus_2250 retrocopy 5' end.
retro_mmus_2250 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2250 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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