RetrogeneDB ID: | retro_mmus_171 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 15:81407195..81408134(-) | ||
| Located in intron of: | ENSMUSG00000022401 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000047108 | |
| Aliases: | Dnajb7, 4933424H20Rik, Dj5, mDj5 | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dnajb6 | ||
| Ensembl ID: | ENSMUSG00000029131 | ||
| Aliases: | Dnajb6, Mrj, mDj4 | ||
| Description: | DnaJ (Hsp40) homolog, subfamily B, member 6 [Source:MGI Symbol;Acc:MGI:1344381] |
Retrocopy-Parental alignment summary:
>retro_mmus_171
ATGGTGGACTATTATGAAGTTCTAGGAGTGCAGAGATATGCGTCACCAGAAGACATTAAAAGAGCTTATCGTAAAGTAGC
ACTTAAATGGCATCCTGATAAAAATCCAGAAAATAAAGAGGAAGCGGAGCGAAAATTCAAAGAAGTCGCCGAGGCATATG
AAGTGTTATCAAATGTTGAGAAACGGGACATTTATGACAAATACGGCAAGGAAGGATTAGACGGCAGAGGTGCAAGCCAT
CTCGACGATGAGCGTGAGTACCGCTTCACATTCCGGAAGGCAGACGATGTCTTTAAGGAAATTTTTGGTGAAAGGGATCC
GTTTTCATTCCACCTCTTTGAGGACTCCCTCGAGGGCCTTTTAAACAGTTCAAGAAGCCCCAGTGGAAGCAGAGGCAGAG
GCGCAGGGTCCCACGTCTCCCGCGCCTATGACCACCCAGCGCTTTCCGGGCTCTCCTCTTACGACACAGGGTATTCATCT
TATGTTTCATTGGGGCATGAGGGCCTTACGTCATTCTCTTCCCTGGCACTTGATGATTCTGGAATGGGCAACTATATACC
CATTACACCTTCAGGCAAAGTTATTAATGGAAGAAATATTAATACAAAGAAAGCTTTTGAGAACCGTCAAGAAAGAGAAG
CTGAAGATGACAGTGAGTTGATATCCTTTCTTGTAAATAGTGTGGCAAATGAAGAGCATTTTACAGACAAATGTAACTGG
AGAAGACAGTCGTTCAACAATTACTCACCAAATTCCTACAGCTCCTCAAATACAACTCAATATACTCTGGTGGACAACAA
TGAACAAGGAACATCTTGGGTCACCAACAAGAAGGAACCTTCCATTTTCTCAGCAGGATTTAAAGAAGGTGGTAGGAGGA
AAAAGAAGAAGCACAAAGAGGGGCAGAAGAAGAAGAAGTCCAACAAAAGGAATCACTAA
ORF - retro_mmus_171 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.68 % |
| Parental protein coverage: | 67.95 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVDYYEVLGVQRHASPEDIKKAYRKQALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGK |
| MVDYYEVLGVQR.ASPEDIK.AYRK.ALKWHPDKNPENKEEAERKFK.VAEAYEVLS...KRDIYDKYGK | |
| Retrocopy | MVDYYEVLGVQRYASPEDIKRAYRKVALKWHPDKNPENKEEAERKFKEVAEAYEVLSNVEKRDIYDKYGK |
| Parental | EGLNGGGGGGGIHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFFEDPFDDFFGNRRGPRGNRSRGAGS |
| EGL.G.G.....H.D...E..FTFR..DDVF.E.FG.RDPFSF..FED.........R.P.G.R.RGAGS | |
| Retrocopy | EGLDGRGAS---HLDDEREYRFTFRKADDVFKEIFGERDPFSFHLFEDSLEGLLNSSRSPSGSRGRGAGS |
| Parental | FFSTFSGFPSFGSGFPAFDTGFTPFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKIVNGKKITTKRIV |
| ..S.....P...SG....DTG.....SLGH.GLTSFSS.....SGMGN...I..S.K..NG..I.TK... | |
| Retrocopy | HVSRAYDHPAL-SGLSSYDTGYSSYVSLGHEGLTSFSSLALDDSGMGNYIPITPSGKVINGRNINTKKAF |
| Parental | ENGQERVEVEEDGQLKSLTINGVADENALAEECQRRGQ |
| EN.QER.E.E.D..L.S...N.VA.E......C..R.Q | |
| Retrocopy | ENRQER-EAEDDSELISFLVNSVANEEHFTDKCNWRRQ |
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 .12 RPM | 19 .16 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 16 .15 RPM |
| SRP007412_heart | 0 .03 RPM | 13 .64 RPM |
| SRP007412_kidney | 0 .17 RPM | 16 .34 RPM |
| SRP007412_liver | 0 .38 RPM | 18 .11 RPM |
| SRP007412_testis | 77 .57 RPM | 121 .39 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_171 was not detected
No EST(s) were mapped for retro_mmus_171 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_42760 | 1067 libraries | 1 library | 1 library | 1 library | 2 libraries |
| TSS #2 | TSS_42761 | 1065 libraries | 2 libraries | 2 libraries | 0 libraries | 3 libraries |
| TSS #3 | TSS_42762 | 1064 libraries | 2 libraries | 1 library | 2 libraries | 3 libraries |
The graphical summary, for retro_mmus_171 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_171 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_171 has 4 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Homo sapiens | retro_hsap_103 |
| Gorilla gorilla | retro_ggor_210 |
| Macaca mulatta | retro_mmul_165 |
| Rattus norvegicus | retro_rnor_212 |