RetrogeneDB ID: | retro_mmus_113 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:88204949..88205678(-) | ||
| Located in intron of: | ENSMUSG00000090165 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081984 | |
| Aliases: | Dnajb3, Hsj3, MSJ-1, Msj1 | ||
| 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_113
ATGGTGGACTACTACGAGGTGCTGGGCGTGCCGCGGCAGGCCTCAGCCGAGGCCATCCGCAAGGCGTACCGCAAGCTTGC
GCTCAAGTGGCACCCGGACAAGAACCCCGAGCACAAGGAGGAGGCCGAGAGGCGGTTCAAGCAGGTGGCGCAGGCCTACG
AGGTCTTATCGGACGTCCGCAAGCGCGAGGTGTACGACCGCTGCGGCGAAGTGGGCGAGGTGGGCGGAGGCGGCGCGGCG
GGCAGCCCGTTCCACGATGCCTTCCAGTACGTCTTCTCCTTCCGAGACCCCGCGGAGGTCTTCAGGGAGTTCTTCGGGGG
CCACGACCCTTTCTCCTTCGACTTCTTCGGGGGAGACCCCCTTGAGAACTTTTTTGGGGATCGGAGGAGCACCCGTGGAA
GCAGAAGCCGAGGGGCTGTACCCTTCTCTACCTCCTTTACCGAATTCCCAGGATTTGGGGGTGGCTTCGCTTCGTTAGAT
ACTGGATTCACATCCTTCGGTTCTCCAGGAAACTCGGGCCTTTCTTCTTTCTCCATGTCTTGCGGCGGTGGGGCGGCAGG
CAACTACAAGTCGGTGTCAACCTCCACCGAAATAATTAATGGCAAAAAAATCACCACCAAGAGAATCGTTGAGAATGGTC
AAGAAAGGGTGGAAGTGGAAGAAGATGGAGAGTTAAAGTCCCTGATAATTAATGGCAAAGAGCAGCTGCTTCGCATCAAT
ACTCAGTAA
ORF - retro_mmus_113 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.31 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVDYYEVLGVQRHASPEDIKKAYRKQALKWHPDKNPENKEEAERKFKQVAEAYEVLSDAKKRDIYDKYGK |
| MVDYYEVLGV.R.AS.E.I.KAYRK.ALKWHPDKNPE.KEEAER.FKQVA.AYEVLSD..KR..YD..G. | |
| Retrocopy | MVDYYEVLGVPRQASAEAIRKAYRKLALKWHPDKNPEHKEEAERRFKQVAQAYEVLSDVRKREVYDRCGE |
| Parental | EGLNGGGGGGGIHFDSPFEFGFTFRNPDDVFREFFGGRDPFSFDFF-EDPFDDFFGNRRGPRGNRSRGAG |
| .G..GGGG..G..F...F...F.FR.P..VFREFFGG.DPFSFDFF..DP...FFG.RR..RG.RSRGA. | |
| Retrocopy | VGEVGGGGAAGSPFHDAFQYVFSFRDPAEVFREFFGGHDPFSFDFFGGDPLENFFGDRRSTRGSRSRGAV |
| Parental | SFFSTFSGFPSFGSGFPAFDTGFTPFGSLGHGGLTSFSSTSFGGSGMGNFKSISTSTKIVNGKKITTKRI |
| .F...F..FP.FG.GF...DTGFT.FGS.G..GL.SF.S.S.GG...GN.KS.STST.I.NGKKITTKRI | |
| Retrocopy | PFSTSFTEFPGFGGGFASLDTGFTSFGSPGNSGLSSF-SMSCGGGAAGNYKSVSTSTEIINGKKITTKRI |
| Parental | VENGQERVEVEEDGQLKSLTINGKEHLLRLDNK |
| VENGQERVEVEEDG.LKSL.INGKE.LLR.... | |
| Retrocopy | VENGQERVEVEEDGELKSLIINGKEQLLRINTQ |
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 .35 RPM | 19 .16 RPM |
| SRP007412_cerebellum | 0 .26 RPM | 16 .15 RPM |
| SRP007412_heart | 0 .09 RPM | 13 .64 RPM |
| SRP007412_kidney | 0 .50 RPM | 16 .34 RPM |
| SRP007412_liver | 0 .22 RPM | 18 .11 RPM |
| SRP007412_testis | 435 .48 RPM | 121 .39 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_113 was not detected
No EST(s) were mapped for retro_mmus_113 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_77437 | 486 libraries | 218 libraries | 316 libraries | 40 libraries | 12 libraries |
| TSS #2 | TSS_77438 | 777 libraries | 267 libraries | 23 libraries | 1 library | 4 libraries |
The graphical summary, for retro_mmus_113 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_113 was not experimentally validated.