RetrogeneDB ID:

retro_mmus_2330

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:4:20073372..20073542(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Smagp
Ensembl ID:ENSMUSG00000053559
Aliases:None
Description:small cell adhesion glycoprotein [Source:MGI Symbol;Acc:MGI:2448476]


Retrocopy-Parental alignment summary:






>retro_mmus_2330
ATGAACAACCTACCGGCCACACCTTCTCTTTAAGAATTGATGACCATGCCAGTTTTTCAGGCCCCCGTGACCCTGTCCGC
ACAAGCTGAAGAGGCCAGCATCGCATTCATTGCAGCTGTTATCACCGTGGTGTTCCTTACCCTGCTCTCAGTGTGACCTT
GATCTTCTTT

ORF - retro_mmus_2330 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.48 %
Parental protein coverage: 58.76 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNNLPATPSPEELMTTPVFQAPETLSPQAEEASTALIAVVITVVFLTLLSV-VTLIFF
MNNLPATPS..ELMT.PVFQAP.TLS.QAEEAS.A.IA.VITVVFLTLLSV.VTLIFF
RetrocopyMNNLPATPSL*ELMTMPVFQAPVTLSAQAEEASIAFIAAVITVVFLTLLSV<VTLIFF

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 0 .96 RPM
SRP007412_cerebellum 0 .04 RPM 0 .87 RPM
SRP007412_heart 0 .00 RPM 6 .41 RPM
SRP007412_kidney 0 .00 RPM 25 .56 RPM
SRP007412_liver 0 .00 RPM 9 .83 RPM
SRP007412_testis 0 .00 RPM 1 .37 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2330 was not detected
No EST(s) were mapped for retro_mmus_2330 retrocopy.
No TSS is located nearby retro_mmus_2330 retrocopy 5' end.
retro_mmus_2330 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2330 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000019831 retrocopy
Callithrix jacchus ENSCJAG000000176801 retrocopy
Dasypus novemcinctus ENSDNOG000000248931 retrocopy
Mus musculus ENSMUSG00000053559 2 retrocopies
retro_mmus_2330 , retro_mmus_3329,



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