RetrogeneDB ID: | retro_mmus_1565 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
Coordinates: | 17:34392415..34392687(+) | ||
Located in intron of: | ENSMUSG00000082103 | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000083522 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | 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] |
Percent Identity: | 79.17 % |
Parental protein coverage: | 96.88 % |
Number of stop codons detected: | 0 |
Number of frameshifts detected | 2 |
Parental | RKVSADGAAKAEPKRRSARLSAKPAPAKVDAKP-KKAAGKDKASDKK-VQIKGKRGAKGKQ-ADVADQQT |
R...ADGA.KAEPKRRSARL.AKPAP....AKP.KKAAGKDKASDKK.VQIKGKRGAKGKQ.A...DQQT | |
Retrocopy | RLAGADGAMKAEPKRRSARLLAKPAP----AKP>KKAAGKDKASDKK>VQIKGKRGAKGKQQAEATDQQT |
Parental | TELPAENGETENQSPASEEEKEAKSD |
T.LP.E.GETENQSPASEEEK.AK.D | |
Retrocopy | TDLPLEDGETENQSPASEEEKGAKFD |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
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 .05 RPM | 25 .52 RPM |
ENCODE library ID | Target | ChIP-Seq Peak coordinates |
---|---|---|
ENCFF001YIJ | POLR2A | 17:34392306..34392514 |
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_52900 | 470 libraries | 421 libraries | 178 libraries | 3 libraries | 0 libraries |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Cavia porcellus | ENSCPOG00000002336 | 7 retrocopies | |
Monodelphis domestica | ENSMODG00000020972 | 5 retrocopies | |
Mus musculus | ENSMUSG00000040681 | 13 retrocopies | |
Rattus norvegicus | ENSRNOG00000048226 | 8 retrocopies | |
Rattus norvegicus | ENSRNOG00000050978 | 5 retrocopies |