General information for g4510.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribonucleoside-diphosphate reductase large subunit.
Parent gene
- The parent gene g4510 is located on chr_2: 2947091..2948718 (- 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 | g4510 | g4510.t1 | TTS | g4510.t1 | 2944656 | 2944656 |
| chr_2 | g4510 | g4510.t1 | isoform | g4510.t1 | 2944813 | 2947487 |
| chr_2 | g4510 | g4510.t1 | exon | g4510.t1.exon1 | 2944813 | 2946386 |
| chr_2 | g4510 | g4510.t1 | cds | g4510.t1.CDS1 | 2944813 | 2946386 |
| chr_2 | g4510 | g4510.t1 | exon | g4510.t1.exon2 | 2946448 | 2946911 |
| chr_2 | g4510 | g4510.t1 | cds | g4510.t1.CDS2 | 2946448 | 2946911 |
| chr_2 | g4510 | g4510.t1 | exon | g4510.t1.exon3 | 2946980 | 2947400 |
| chr_2 | g4510 | g4510.t1 | cds | g4510.t1.CDS3 | 2946980 | 2947400 |
| chr_2 | g4510 | g4510.t1 | exon | g4510.t1.exon4 | 2947469 | 2947487 |
| chr_2 | g4510 | g4510.t1 | cds | g4510.t1.CDS4 | 2947469 | 2947487 |
| chr_2 | g4510 | g4510.t1 | TSS | g4510.t1 | 2947652 | 2947652 |
Sequences
>g4510.t1 Gene=g4510 Length=2478
ATGTTTGTCATAAAGAGAGACGGACGCAAGGAGGAAGTTCATTTTGATAAAATAACTTCG
AGAATACAAAAACTTTGCTATGGATTGAATATGGATTTTGTTGATCCCGTATCAATTACT
CTTAAAGTTATTAATGGTCTCTTCTCCGGTGTAACAACTCAAGAATTGGATAATTTGGCA
GCTGAAACAGCCGCAACAATGACAACCGATCATGCTGATTATGCAGTTTTAGCTGCTCGC
ATTGCTGTCTCTAATCTACACAAAGAGACAAAAAAACAATTCAGCGATGTCATGGATGAT
CTTTATAATATGGAAAATGAATTTTTGAAAACAAAATCTCCGATGATTAGTGAATATCAT
CACAACATTATTATGAAGAATGCAGATCGACTGAATTCGGCCATCATTTATGATCGTGAT
TTCGGATACAATTATTTTGGTTTTAAAACACTCGAGAGAAGCTATTTACTTAAGATTAAG
GGTAAAATTGTTGAGAGACCTCAACATATGCTTATGCGAGTTGCCGTAGGCATACATGGA
GAAGACATTGATGCAGCAATTGAAACATATAATCTTCTTTCAGAAAGATATTTTACTCAT
GCATCACCAACACTTTTTGCAGCTGCAACTCCTCGTCCACAACTTTCTTCTTGCTTCCTA
CTTTCAATGTCAGATGATTCAATTGAAGGTATTTATGATACATTAAAACAATGCGCACTT
ATTAGCAAATCTGCCGGTGGAATCGGTTTAAATGTTCATTGTATTCGGGCAAAAGGGACT
TACATTGCTGGAACAAATGGAATTTCAAATGGGCTTGTTCCCATGTTGAGAGTTTACAAT
AACACAGCAAGATATGTTGATCAAGGAGGAAACAAAAGACCAGGTGCTTTTGCTGTTTAT
TTGGAACCATGGCATGGAGATATCTTTGAATTTTTGGATTTGAAAAAGAATACTGGAAAA
GAAGAAGTAAGAGCAAGAGACATGTTTTATGCTTTATGGATACCTGATTTGTTTATGCGT
CGTGTTGAGAATAATGAAATGTGGAGTTTAATGTGTCCACATAGCTGTCCAGGATTGTAC
GATACGTGGGGAGAAGAATTTGAAAAAATTTATGAGAAATATGAGGCAGAAGGTCGCTAT
ATTCGTCAAATTAAAGCACAAGATTTATGGTTTGCAATTATTGAGTCTCAAGTTGAAACT
GGAACACCATATATGCTTTATAAAGATGCATGCAATCGTAAATCAAATCAACAAAATCTT
GGAACAATTCGATGCTCCAATCTCTGTACAGAAATTGTCGAGTATTCTAGCAAAGATGAA
ATTGCTGTTTGTAATTTGGCTTCAATTGCTCTCAACATGTTTGTTAAAGCAAATAGAAAG
GAGTACGATTTCGATAAATTGAAAGAAGTTGCAAAAATTGCAACGAAAAATTTGAATAAA
ATCATTGATGTCAATTATTATCCGGTTGAAGAGGCTAAACGTTCAAATATGAGACATCGT
CCAATTGGCATTGGTGTACAAGGATTAGCTGATACTTTTATTATTATGAGAATGCCTTAT
GAATCTCTCGAAGCAAGAAAATTGAATGAGCAAATCTTTGAAACCATTTATTATGGTGCA
CTTGAGGCTAGCTGTGAGTTGGCTGAAAAATTAGGACCATATGAAACTTATGAAGGTAGT
CCCGTTTCAAAGGGTATTTTGCAGTATGATATGTGGGATAAGACACCGAGTGATTTATGG
GATTGGGCTGCTTTGAAAGCAAAAATTGCTAAATATGGTGTTAGAAATTCATTGTTGATT
GCACCGATGCCCACTGCATCGACTGCACAAATTTTGGGTAATAATGAGAGTTTTGAACCA
TATACTAGTAACGTCTATAATCGTCGTGTTTTAAGTGGAGAATTTCAAGTTGTCAATCAT
CATTTAATTAAAGACTTAACTGATTGTGGTCTTTGGGATGATGACATGAAAAACAGAATC
ATTGCAAATAATGGATCGATTCAACAGATTGAAGAGATTCCAGAGCATATTCGAAACATT
TACAAAACAGTTTGGGAAATTTCTGTCAAGAATCAAATTCAGATGGCTGCTGATCGTGGT
GCATATATTGATCAAAGTCAATCTTTCAATATTCATGTTGCTGAACCCAATTATGGAAAA
TTGACATCAATTCATTTTTATGGTTGGAAATTGGGACTTAAAACGGGAATGTATTATTTA
AGAACAAAACCAGCTGCAAATGCAATTCAATTTACAGTTGATAAAAATCGCTTAAATCAG
CCTGTTACAAATACTTCTACAACAAATGGTCATCATGCAAATAACGAATCTAATTCATCG
TCTGCCAAAAACTCACCAAATGTATCGCTCAATGGAACATTAAATGAAAACGGAGATACT
AGTGAACGTGAAGCTCGTATTGCTCAAATGGTATGCTCATTGGAAAATAAGGACGAATGC
TTGATGTGTGGTTCTTAA
>g4510.t1 Gene=g4510 Length=825
MFVIKRDGRKEEVHFDKITSRIQKLCYGLNMDFVDPVSITLKVINGLFSGVTTQELDNLA
AETAATMTTDHADYAVLAARIAVSNLHKETKKQFSDVMDDLYNMENEFLKTKSPMISEYH
HNIIMKNADRLNSAIIYDRDFGYNYFGFKTLERSYLLKIKGKIVERPQHMLMRVAVGIHG
EDIDAAIETYNLLSERYFTHASPTLFAAATPRPQLSSCFLLSMSDDSIEGIYDTLKQCAL
ISKSAGGIGLNVHCIRAKGTYIAGTNGISNGLVPMLRVYNNTARYVDQGGNKRPGAFAVY
LEPWHGDIFEFLDLKKNTGKEEVRARDMFYALWIPDLFMRRVENNEMWSLMCPHSCPGLY
DTWGEEFEKIYEKYEAEGRYIRQIKAQDLWFAIIESQVETGTPYMLYKDACNRKSNQQNL
GTIRCSNLCTEIVEYSSKDEIAVCNLASIALNMFVKANRKEYDFDKLKEVAKIATKNLNK
IIDVNYYPVEEAKRSNMRHRPIGIGVQGLADTFIIMRMPYESLEARKLNEQIFETIYYGA
LEASCELAEKLGPYETYEGSPVSKGILQYDMWDKTPSDLWDWAALKAKIAKYGVRNSLLI
APMPTASTAQILGNNESFEPYTSNVYNRRVLSGEFQVVNHHLIKDLTDCGLWDDDMKNRI
IANNGSIQQIEEIPEHIRNIYKTVWEISVKNQIQMAADRGAYIDQSQSFNIHVAEPNYGK
LTSIHFYGWKLGLKTGMYYLRTKPAANAIQFTVDKNRLNQPVTNTSTTNGHHANNESNSS
SAKNSPNVSLNGTLNENGDTSEREARIAQMVCSLENKDECLMCGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g4510.t1 | CDD | cd01679 | RNR_I | 167 | 742 | 0.0 |
| 13 | g4510.t1 | Gene3D | G3DSA:3.20.70.20 | - | 74 | 750 | 0.0 |
| 16 | g4510.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 765 | 789 | - |
| 4 | g4510.t1 | PANTHER | PTHR11573 | RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE LARGE CHAIN | 1 | 824 | 0.0 |
| 10 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 293 | 312 | 2.7E-68 |
| 7 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 423 | 434 | 2.7E-68 |
| 8 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 462 | 485 | 2.7E-68 |
| 5 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 500 | 522 | 2.7E-68 |
| 6 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 528 | 551 | 2.7E-68 |
| 9 | g4510.t1 | PRINTS | PR01183 | Ribonucleotide reductase large chain signature | 593 | 620 | 2.7E-68 |
| 3 | g4510.t1 | Pfam | PF03477 | ATP cone domain | 1 | 89 | 2.0E-19 |
| 2 | g4510.t1 | Pfam | PF00317 | Ribonucleotide reductase, all-alpha domain | 143 | 212 | 3.3E-22 |
| 1 | g4510.t1 | Pfam | PF02867 | Ribonucleotide reductase, barrel domain | 216 | 739 | 5.6E-198 |
| 15 | g4510.t1 | ProSitePatterns | PS00089 | Ribonucleotide reductase large subunit signature. | 582 | 604 | - |
| 18 | g4510.t1 | ProSiteProfiles | PS51161 | ATP-cone domain profile. | 1 | 92 | 21.383 |
| 11 | g4510.t1 | SUPERFAMILY | SSF48168 | R1 subunit of ribonucleotide reductase, N-terminal domain | 6 | 214 | 3.4E-68 |
| 12 | g4510.t1 | SUPERFAMILY | SSF51998 | PFL-like glycyl radical enzymes | 215 | 752 | 5.8E-199 |
| 17 | g4510.t1 | TIGRFAM | TIGR02506 | NrdE_NrdA: ribonucleoside-diphosphate reductase, alpha subunit | 145 | 743 | 1.1E-219 |
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:0004748 | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor | MF |
| GO:0005524 | ATP binding | MF |
| GO:0006260 | DNA replication | BP |
| GO:0055114 | NA | NA |
KEGG
Orthology
- This transcript has been annotated with K10807 (ribonucleoside-diphosphate reductase subunit M1)
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.
