General information for g11955.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Thymidylate synthase.
Parent gene
- The parent gene g11955 is located on chr_1: 19785720..19787708 (- 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_1 | g11955 | g11955.t1 | TTS | g11955.t1 | 19785579 | 19785579 |
| chr_1 | g11955 | g11955.t1 | isoform | g11955.t1 | 19785720 | 19786898 |
| chr_1 | g11955 | g11955.t1 | exon | g11955.t1.exon1 | 19785720 | 19786507 |
| chr_1 | g11955 | g11955.t1 | cds | g11955.t1.CDS1 | 19785720 | 19786507 |
| chr_1 | g11955 | g11955.t1 | exon | g11955.t1.exon2 | 19786580 | 19786769 |
| chr_1 | g11955 | g11955.t1 | cds | g11955.t1.CDS2 | 19786580 | 19786769 |
| chr_1 | g11955 | g11955.t1 | exon | g11955.t1.exon3 | 19786827 | 19786898 |
| chr_1 | g11955 | g11955.t1 | cds | g11955.t1.CDS3 | 19786827 | 19786898 |
| chr_1 | g11955 | g11955.t1 | TSS | g11955.t1 | 19786866 | 19786866 |
Sequences
>g11955.t1 Gene=g11955 Length=1050
ATGAAAAGTGAACAAATTTTTAATTCTGAATCACTGTGTAATCCTGATTTCATTCATAAA
ATTGATAAAATGGAGAATACAGATAATGGAAATTTAACAAATAATTCAACAGAAAACATT
CAAAAACTTAAAGTAAATCAAAAAGTCAATGGATCTCATAATCAGGAAAATTTTGAAGAG
GAGATAGAACATGATGAAGTGCAGTATTTAAATTTAATTCGCAATGTACTGAAACGTGGA
ATAATTCGTGGAGATAGAACTGGTGTTGGTACAATCAGTATTTTCGGTGCACAAATGAGA
TTTAATTTGCGAGATCAATTTCCTTTGCTAACAACTAAAAGAGTTTTTTGGCGAGGACTT
GTTGAAGAATTGCTCTGGTTTATTCAAGGTTCAACAGATGCAAAGCTGTTACAAGCGAAA
AACGTTCGAATTTGGGATGGTAATAGTACCCGAGAGTTTCTCGATGCATCTGGATTTCAT
GATCGTCAAGTTGGTGATTTAGGTCCTGTCTATGGTTTTCAATGGCGGCATTATAGTGCT
GAATATAAAACTTGTAATGACGATTATACTGGTAAAGGTATTGATCAATTAAAAGATGTT
ATCGAGCGTATTAAAACAAATCCAAATGATCGTCGCATTATAATGACTGCATGGAATCCA
GTTGATATTCCAAAGATGGCTCTTCCACCATGTCATTGTCTTGTCCAGTTTTACGTTGCT
AACGGTGAATTGAGTTGTCAATTGTACCAAAGAAGTGCCGATATCGGTCTCGGAGTTCCT
TTCAATATAGCATCATATGCACTCTTGACCTATATGATTGCTCATGTCACAAACTTGAAA
CCAGGTGATTTTGTTCATTCTTTAGGTGATACACATGTTTATCTTAATCACGTAGAGCCT
TTAAAAGAGCAATTGGAACGTAAACCAAAGGCGTTTCCAAAATTAAAAATTAACCGAGAG
GTCGCCAACATTGATGACTTTAAATTCGAAGATTTTGAGTTAATTGGTTACGATCCTTAC
CCCACAATAAAAATGGAAATGGCTGTTTAA
>g11955.t1 Gene=g11955 Length=349
MKSEQIFNSESLCNPDFIHKIDKMENTDNGNLTNNSTENIQKLKVNQKVNGSHNQENFEE
EIEHDEVQYLNLIRNVLKRGIIRGDRTGVGTISIFGAQMRFNLRDQFPLLTTKRVFWRGL
VEELLWFIQGSTDAKLLQAKNVRIWDGNSTREFLDASGFHDRQVGDLGPVYGFQWRHYSA
EYKTCNDDYTGKGIDQLKDVIERIKTNPNDRRIIMTAWNPVDIPKMALPPCHCLVQFYVA
NGELSCQLYQRSADIGLGVPFNIASYALLTYMIAHVTNLKPGDFVHSLGDTHVYLNHVEP
LKEQLERKPKAFPKLKINREVANIDDFKFEDFELIGYDPYPTIKMEMAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11955.t1 | CDD | cd00351 | TS_Pyrimidine_HMase | 68 | 302 | 2.26512E-119 |
| 11 | g11955.t1 | Gene3D | G3DSA:3.30.572.10 | Thymidylate Synthase | 48 | 349 | 4.1E-143 |
| 4 | g11955.t1 | Hamap | MF_00008 | Thymidylate synthase [thyA]. | 66 | 349 | 38.059769 |
| 2 | g11955.t1 | PANTHER | PTHR11548 | THYMIDYLATE SYNTHASE 1 | 24 | 349 | 8.5E-173 |
| 3 | g11955.t1 | PANTHER | PTHR11548:SF2 | THYMIDYLATE SYNTHASE | 24 | 349 | 8.5E-173 |
| 7 | g11955.t1 | PRINTS | PR00108 | Thymidylate synthase family signature | 107 | 128 | 7.7E-54 |
| 8 | g11955.t1 | PRINTS | PR00108 | Thymidylate synthase family signature | 200 | 219 | 7.7E-54 |
| 5 | g11955.t1 | PRINTS | PR00108 | Thymidylate synthase family signature | 226 | 241 | 7.7E-54 |
| 6 | g11955.t1 | PRINTS | PR00108 | Thymidylate synthase family signature | 244 | 270 | 7.7E-54 |
| 9 | g11955.t1 | PRINTS | PR00108 | Thymidylate synthase family signature | 282 | 299 | 7.7E-54 |
| 1 | g11955.t1 | Pfam | PF00303 | Thymidylate synthase | 68 | 349 | 6.8E-119 |
| 13 | g11955.t1 | ProSitePatterns | PS00091 | Thymidylate synthase active site. | 211 | 239 | - |
| 10 | g11955.t1 | SUPERFAMILY | SSF55831 | Thymidylate synthase/dCMP hydroxymethylase | 60 | 349 | 7.2E-141 |
| 14 | g11955.t1 | TIGRFAM | TIGR03284 | thym_sym: thymidylate synthase | 68 | 349 | 9.2E-114 |
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:0006231 | dTMP biosynthetic process | BP |
| GO:0004799 | thymidylate synthase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00560 (thymidylate synthase)
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.
