General information for g6617.t1
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.t1 | TSS | g6617.t1 | 17823834 | 17823834 |
| chr_2 | g6617 | g6617.t1 | isoform | g6617.t1 | 17823921 | 17825507 |
| chr_2 | g6617 | g6617.t1 | exon | g6617.t1.exon1 | 17823921 | 17823992 |
| chr_2 | g6617 | g6617.t1 | cds | g6617.t1.CDS1 | 17823921 | 17823992 |
| chr_2 | g6617 | g6617.t1 | exon | g6617.t1.exon2 | 17824100 | 17824375 |
| chr_2 | g6617 | g6617.t1 | cds | g6617.t1.CDS2 | 17824100 | 17824375 |
| chr_2 | g6617 | g6617.t1 | exon | g6617.t1.exon3 | 17824626 | 17825507 |
| chr_2 | g6617 | g6617.t1 | cds | g6617.t1.CDS3 | 17824626 | 17825507 |
| chr_2 | g6617 | g6617.t1 | TTS | g6617.t1 | 17825681 | 17825681 |
Sequences
>g6617.t1 Gene=g6617 Length=1230
ATGTCTTTAATTAAAATTGTTCAAGAAAAAGAAAACAATATTGCAGACACAATGGAAAAG
TTTTCATTAAAAAGTCCTCGAAAGGTATTGACTGAAAATGAAGTAAATTTACCTTCCAAA
CTTCCAAAGTTGTTGAAAGGAATGGACGATGGTTCACAAGGAACTGAAAATAAAGAAGCT
GACTTGAGCAAAGTCATAAAATCAGAGGAGGCACAAGTTGGTGCAATTGCTCACAAGAAA
AGCACCTATAATTTTGATCCATCACTCGAACCACTGCTACGTGATAATCCAAGACGTTTT
GTCATTTTCCCTATTGAATATTCCGACATTTGGCAAATGTACAAAAAGGCTGAAGCAAGC
TTTTGGACTGTTGAAGAAGTTGATCTCTCTAAAGATATGAATGATTGGAATAATTTAAAA
GATTGTGAACGACATTTTATATCGCATGTATTAGCTTTCTTTGCGGCATCGGATGGAATA
GTAAATGAAAATCTTGTTGAACGCTTTAGTCAAGAAGTTCAAGTAACAGAAGCTCGCTGC
TTTTATGGCTTTCAAATAGCTATGGAAAATGTTCATTCAGAAATGTATTCGTTACTCATT
GAGACTTATGTTCGTGATTCTAAAGAACGTGAATTTCTCTTTAATGCTATTCAAACTTTG
CCTTGTGTTAAAAAGAAAGCAGACTGGGCAATGAATTGGATATCAAGCAAAAACGCAAAT
TTTGGCGAGAGAATCATTGCATTTGCATCTGTCGAGGGTATTTTCTTCAGTGGTAGTTTT
GCTGCAATATTTTGGCTAAAGAAACACGGACTTATACCTGGCTTAACATTTTCGAATGAA
CTTATTTCACGCGATGAAGGCTTACATTGTGACTTTGCATGTCTTATGTTTAAACATTTG
GTTCAGAAGCCACCCAAAGAGAGAATAATTGAAATAATCTCAGAGGCTGTTAAAATTGAA
CAAGAATTTTTAACTGATGCTCTACCTGTCAACATGTTGGGAATGAATTGTGATTTAATG
TCACAATACATAGAATTTGTTGCTGATCGTTTATTAGTAGAGCTAGGCGTCGAAAAAATT
TATAATACAAAGAATCCATTCTCATTTATGGAATTCATTTCTTTAGAAGGAAAAACTAAT
TTCTTTGAGAAAAAAGTTGGAGAATATCAAAAGTATGGAGTCATGTCAAGTCGAAAAGAT
CATGTTTTTACATTAGATGCTGATTTTTGA
>g6617.t1 Gene=g6617 Length=409
MSLIKIVQEKENNIADTMEKFSLKSPRKVLTENEVNLPSKLPKLLKGMDDGSQGTENKEA
DLSKVIKSEEAQVGAIAHKKSTYNFDPSLEPLLRDNPRRFVIFPIEYSDIWQMYKKAEAS
FWTVEEVDLSKDMNDWNNLKDCERHFISHVLAFFAASDGIVNENLVERFSQEVQVTEARC
FYGFQIAMENVHSEMYSLLIETYVRDSKEREFLFNAIQTLPCVKKKADWAMNWISSKNAN
FGERIIAFASVEGIFFSGSFAAIFWLKKHGLIPGLTFSNELISRDEGLHCDFACLMFKHL
VQKPPKERIIEIISEAVKIEQEFLTDALPVNMLGMNCDLMSQYIEFVADRLLVELGVEKI
YNTKNPFSFMEFISLEGKTNFFEKKVGEYQKYGVMSSRKDHVFTLDADF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g6617.t1 | CDD | cd01049 | RNRR2 | 100 | 375 | 1.75593E-137 |
| 6 | g6617.t1 | Gene3D | G3DSA:1.10.620.20 | Ribonucleotide Reductase | 67 | 391 | 4.2E-143 |
| 2 | g6617.t1 | PANTHER | PTHR23409:SF20 | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SUBUNIT M2 | 77 | 409 | 9.3E-196 |
| 3 | g6617.t1 | PANTHER | PTHR23409 | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE SMALL CHAIN | 77 | 409 | 9.3E-196 |
| 1 | g6617.t1 | Pfam | PF00268 | Ribonucleotide reductase, small chain | 99 | 366 | 8.5E-118 |
| 8 | g6617.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 244 | - |
| 9 | g6617.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 245 | 266 | - |
| 7 | g6617.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 267 | 409 | - |
| 5 | g6617.t1 | ProSitePatterns | PS00368 | Ribonucleotide reductase small subunit signature. | 188 | 204 | - |
| 4 | g6617.t1 | SUPERFAMILY | SSF47240 | Ferritin-like | 81 | 391 | 1.69E-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.
