General information for g6617.t13
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribonucleoside-diphosphate reductase subunit M2.
Parent gene
- The parent gene g6617 is located on chr_2: 17825507..17826455 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_2 | g6617 | g6617.t13 | TSS | g6617.t13 | 17823834 | 17823834 |
| chr_2 | g6617 | g6617.t13 | isoform | g6617.t13 | 17823921 | 17825507 |
| chr_2 | g6617 | g6617.t13 | exon | g6617.t13.exon1 | 17823921 | 17824375 |
| chr_2 | g6617 | g6617.t13 | cds | g6617.t13.CDS1 | 17824169 | 17824375 |
| chr_2 | g6617 | g6617.t13 | exon | g6617.t13.exon2 | 17824626 | 17825507 |
| chr_2 | g6617 | g6617.t13 | cds | g6617.t13.CDS2 | 17824626 | 17825507 |
| chr_2 | g6617 | g6617.t13 | TTS | g6617.t13 | 17825681 | 17825681 |
Sequences
>g6617.t13 Gene=g6617 Length=1337
ATGTCTTTAATTAAAATTGTTCAAGAAAAAGAAAACAATATTGCAGACACAATGGAAAAG
TTTTCATTAAAAGTAAGTGCAAAACAACTATAAAATTTCAATTTTCCCACCAAAAAGTTT
AACCTTGCTTAAAAATCTATCGATAAATTACAATTATTTTTCAATATTCTTATATATAGA
GTCCTCGAAAGGTATTGACTGAAAATGAAGTAAATTTACCTTCCAAACTTCCAAAGTTGT
TGAAAGGAATGGACGATGGTTCACAAGGAACTGAAAATAAAGAAGCTGACTTGAGCAAAG
TCATAAAATCAGAGGAGGCACAAGTTGGTGCAATTGCTCACAAGAAAAGCACCTATAATT
TTGATCCATCACTCGAACCACTGCTACGTGATAATCCAAGACGTTTTGTCATTTTCCCTA
TTGAATATTCCGACATTTGGCAAATGTACAAAAAGGCTGAAGCAAGCTTTTGGACTGTTG
AAGAAGTTGATCTCTCTAAAGATATGAATGATTGGAATAATTTAAAAGATTGTGAACGAC
ATTTTATATCGCATGTATTAGCTTTCTTTGCGGCATCGGATGGAATAGTAAATGAAAATC
TTGTTGAACGCTTTAGTCAAGAAGTTCAAGTAACAGAAGCTCGCTGCTTTTATGGCTTTC
AAATAGCTATGGAAAATGTTCATTCAGAAATGTATTCGTTACTCATTGAGACTTATGTTC
GTGATTCTAAAGAACGTGAATTTCTCTTTAATGCTATTCAAACTTTGCCTTGTGTTAAAA
AGAAAGCAGACTGGGCAATGAATTGGATATCAAGCAAAAACGCAAATTTTGGCGAGAGAA
TCATTGCATTTGCATCTGTCGAGGGTATTTTCTTCAGTGGTAGTTTTGCTGCAATATTTT
GGCTAAAGAAACACGGACTTATACCTGGCTTAACATTTTCGAATGAACTTATTTCACGCG
ATGAAGGCTTACATTGTGACTTTGCATGTCTTATGTTTAAACATTTGGTTCAGAAGCCAC
CCAAAGAGAGAATAATTGAAATAATCTCAGAGGCTGTTAAAATTGAACAAGAATTTTTAA
CTGATGCTCTACCTGTCAACATGTTGGGAATGAATTGTGATTTAATGTCACAATACATAG
AATTTGTTGCTGATCGTTTATTAGTAGAGCTAGGCGTCGAAAAAATTTATAATACAAAGA
ATCCATTCTCATTTATGGAATTCATTTCTTTAGAAGGAAAAACTAATTTCTTTGAGAAAA
AAGTTGGAGAATATCAAAAGTATGGAGTCATGTCAAGTCGAAAAGATCATGTTTTTACAT
TAGATGCTGATTTTTGA
>g6617.t13 Gene=g6617 Length=362
MDDGSQGTENKEADLSKVIKSEEAQVGAIAHKKSTYNFDPSLEPLLRDNPRRFVIFPIEY
SDIWQMYKKAEASFWTVEEVDLSKDMNDWNNLKDCERHFISHVLAFFAASDGIVNENLVE
RFSQEVQVTEARCFYGFQIAMENVHSEMYSLLIETYVRDSKEREFLFNAIQTLPCVKKKA
DWAMNWISSKNANFGERIIAFASVEGIFFSGSFAAIFWLKKHGLIPGLTFSNELISRDEG
LHCDFACLMFKHLVQKPPKERIIEIISEAVKIEQEFLTDALPVNMLGMNCDLMSQYIEFV
ADRLLVELGVEKIYNTKNPFSFMEFISLEGKTNFFEKKVGEYQKYGVMSSRKDHVFTLDA
DF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6617.t13 | CDD | cd01049 | RNRR2 | 53 | 328 | 1.70619E-137 |
| 5 | g6617.t13 | Gene3D | G3DSA:1.10.620.20 | Ribonucleotide Reductase | 20 | 344 | 2.7E-143 |
| 2 | g6617.t13 | PANTHER | PTHR23409:SF20 | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 | 36 | 362 | 4.5E-195 |
| 3 | g6617.t13 | PANTHER | PTHR23409 | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN | 36 | 362 | 4.5E-195 |
| 9 | g6617.t13 | PIRSF | PIRSF000355 | NrdB | 38 | 354 | 8.8E-71 |
| 1 | g6617.t13 | Pfam | PF00268 | Ribonucleotide reductase, small chain | 52 | 319 | 5.8E-118 |
| 7 | g6617.t13 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 197 | - |
| 8 | g6617.t13 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 198 | 219 | - |
| 6 | g6617.t13 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 220 | 362 | - |
| 11 | g6617.t13 | ProSitePatterns | PS00368 | Ribonucleotide reductase small subunit signature. | 141 | 157 | - |
| 4 | g6617.t13 | SUPERFAMILY | SSF47240 | Ferritin-like | 34 | 344 | 1.15E-121 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0009263 | deoxyribonucleotide biosynthetic process | BP |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10808 (ribonucleoside-diphosphate reductase subunit M2)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
