RetrogeneDB ID:

retro_mmus_2895

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:11866596..11866855(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Hmgn1
Ensembl ID:ENSMUSG00000040681
Aliases:None
Description:high mobility group nucleosomal binding domain 1 [Source:MGI Symbol;Acc:MGI:96120]


Retrocopy-Parental alignment summary:






>retro_mmus_2895
CAGAGGAAGGTTAGCAGGGATGGAGCTGCAAAGACGGAACCCAAGTGCCTCTGCGAGGCTGTTGACTAAGCCCGCCCTTC
GACCGACCTTGGGAAAGGATAAAGCATCAGACAAAAAAGTGCAAATAAAAGGGAAGAGGGGAGTGAAGGGCAAACAGGCT
GACGTGGCTGACCAGTAAACCATAGATCTGCCTGCAGAAAATGGAGAGACAGAAAACCAGAGTCTAGCCTCTGAAGAATA
GAAAGAAGCCAAGTCCAAC

ORF - retro_mmus_2895 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.41 %
Parental protein coverage: 97.67 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalKRKVSADGAAKAEKP-APAKVDAKP--KKAAGKDKASDKKVQIKGKRGAKGKQADVADQQTTELPAENGE
.RKVS.DGAAK.E...A.A....KP......GKDKASDKKVQIKGKRG.KGKQADVADQ.T..LPAENGE
RetrocopyQRKVSRDGAAKTEPK>ASARLLTKPALRPTLGKDKASDKKVQIKGKRGVKGKQADVADQ*TIDLPAENGE
ParentalTENQSPASEEEKEAKSD
TENQS.ASEE.KEAKS.
RetrocopyTENQSLASEE*KEAKSN

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 .00 RPM 27 .59 RPM
SRP007412_cerebellum 0 .00 RPM 26 .14 RPM
SRP007412_heart 0 .00 RPM 21 .23 RPM
SRP007412_kidney 0 .02 RPM 50 .01 RPM
SRP007412_liver 0 .00 RPM 36 .43 RPM
SRP007412_testis 0 .00 RPM 25 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2895 was not detected
No EST(s) were mapped for retro_mmus_2895 retrocopy.
No TSS is located nearby retro_mmus_2895 retrocopy 5' end.
retro_mmus_2895 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2895 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000023367 retrocopies
Monodelphis domestica ENSMODG000000209725 retrocopies
Mus musculus ENSMUSG00000040681 13 retrocopies
Rattus norvegicus ENSRNOG000000482268 retrocopies
Rattus norvegicus ENSRNOG000000509785 retrocopies



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