RetrogeneDB ID: | retro_mmus_2843 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:81840820..81841362(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Hmgb2 | ||
| Ensembl ID: | ENSMUSG00000054717 | ||
| Aliases: | Hmgb2, C80539, HMG-2, Hmg2 | ||
| Description: | high mobility group box 2 [Source:MGI Symbol;Acc:MGI:96157] |
Retrocopy-Parental alignment summary:
>retro_mmus_2843
ATGGGCAAGGGTGACCCCAACAAGCCGTGCAGCAAAATGTCCTCATAGCCTTCTTCATGCAGACCTGCCTGGAGGAGCAC
AAGAAGAAGCATCCAGACTCATCGGCCAGCTTGGCCGAGTTCTCCAAGAAGTGATCCGAGAGATGGAACACTATGTCTGC
AAAGGAAAAGTCGAAGTTTGAAGATTTGGCCAAGAGCGACAAAGCACGTTATGACAGGGAGATGAAGAACTATGTTCCTT
CCAAAGGTGATAAGAAAGGAAAGAAAAAAGATCCAAATGCTCCGAAGAGACCACCATCTGCCTTCTTCCTGTTTTGCTCT
GAAAATCGCCCAGAGATTAAAATTGATCACCCTGGCTTGTCTATTGGAGATACTTCGAAGAAACTGGGTGTGATGTGGTC
TGAACAATCTGCCAAAGATAAACAACCATATGAGCAGAAAGCAGCTAAACCAAAGGAGAAGTATGAAAAGGATATTGCTG
CATTCCGTGCCAAGGGCAAAAGTGAAGCAGGAAAGAAGGGTTCTGATAGGCCAACAGGCTCA
ORF - retro_mmus_2843 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.01 % |
| Parental protein coverage: | 86.19 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MGKGDPNKPRGKMSS-YAFFVQTCREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDLAKSDKA |
| MGKGDPNKP..KMSS..AFF.QTC.EEHKKKHPDSS...AEFSKK.SERW.TMSAKEKSKFEDLAKSDKA | |
| Retrocopy | MGKGDPNKPCSKMSS<IAFFMQTCLEEHKKKHPDSSASLAEFSKK*SERWNTMSAKEKSKFEDLAKSDKA |
| Parental | RYDREMKNYVPPKGDKKGKKKDPNAPKRPPSAFFLFCSENRPKIKIEHPGLSIGDTAKKLGEMWSEQSAK |
| RYDREMKNYVP.KGDKKGKKKDPNAPKRPPSAFFLFCSENRP.IKI.HPGLSIGDT.KKLG.MWSEQSAK | |
| Retrocopy | RYDREMKNYVPSKGDKKGKKKDPNAPKRPPSAFFLFCSENRPEIKIDHPGLSIGDTSKKLGVMWSEQSAK |
| Parental | DKQPYEQKAAKLKEKYEKDIAAYRAKGKSEAGKKGPGRPTGS |
| DKQPYEQKAAK.KEKYEKDIAA.RAKGKSEAGKKG..RPTGS | |
| Retrocopy | DKQPYEQKAAKPKEKYEKDIAAFRAKGKSEAGKKGSDRPTGS |
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 | 1 .89 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 1 .95 RPM |
| SRP007412_heart | 0 .00 RPM | 4 .83 RPM |
| SRP007412_kidney | 0 .00 RPM | 8 .49 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .51 RPM |
| SRP007412_testis | 0 .00 RPM | 37 .37 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2843 was not detected
No EST(s) were mapped for retro_mmus_2843 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_124794 | 754 libraries | 299 libraries | 18 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_2843 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_2843 was not experimentally validated.