General information for g11955.t2
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.t2 | isoform | g11955.t2 | 19783478 | 19786898 |
| chr_1 | g11955 | g11955.t2 | exon | g11955.t2.exon1 | 19783478 | 19783533 |
| chr_1 | g11955 | g11955.t2 | exon | g11955.t2.exon2 | 19785635 | 19786507 |
| chr_1 | g11955 | g11955.t2 | cds | g11955.t2.CDS1 | 19785720 | 19786475 |
| chr_1 | g11955 | g11955.t2 | exon | g11955.t2.exon3 | 19786580 | 19786898 |
| chr_1 | g11955 | g11955.t2 | TSS | g11955.t2 | 19786866 | 19786866 |
| chr_1 | g11955 | g11955.t2 | TTS | g11955.t2 | NA | NA |
Sequences
>g11955.t2 Gene=g11955 Length=1248
ATGAAAAGTGAACAAATTTTTAATTCTGAATCACTGTGTAATCCTGATTTCATTCATAAA
ATTGATAAAATGGTAAGATAAAATACTACATGTGCTGTATAATTTATTATCATTAAAAAT
TTTTGGCAGGAGAATACAGATAATGGAAATTTAACAAATAATTCAACAGAAAACATTCAA
AAACTTAAAGTAAATCAAAAAGTCAATGGATCTCATAATCAGGAAAATTTTGAAGAGGAG
ATAGAACATGATGAAGTGCAGTATTTAAATTTAATTCGCAATGTACTGAAACGTGGAATA
ATTCGTGGAGATAGAACTGGTGTTGGTACAATCAGTATTTTCGGTGCACAAATGAGATTT
AATTTGCGAGATCAATTTCCTTTGCTAACAACTAAAAGAGTTTTTTGGCGAGGACTTGTT
GAAGAATTGCTCTGGTTTATTCAAGGTTCAACAGATGCAAAGCTGTTACAAGCGAAAAAC
GTTCGAATTTGGGATGGTAATAGTACCCGAGAGTTTCTCGATGCATCTGGATTTCATGAT
CGTCAAGTTGGTGATTTAGGTCCTGTCTATGGTTTTCAATGGCGGCATTATAGTGCTGAA
TATAAAACTTGTAATGACGATTATACTGGTAAAGGTATTGATCAATTAAAAGATGTTATC
GAGCGTATTAAAACAAATCCAAATGATCGTCGCATTATAATGACTGCATGGAATCCAGTT
GATATTCCAAAGATGGCTCTTCCACCATGTCATTGTCTTGTCCAGTTTTACGTTGCTAAC
GGTGAATTGAGTTGTCAATTGTACCAAAGAAGTGCCGATATCGGTCTCGGAGTTCCTTTC
AATATAGCATCATATGCACTCTTGACCTATATGATTGCTCATGTCACAAACTTGAAACCA
GGTGATTTTGTTCATTCTTTAGGTGATACACATGTTTATCTTAATCACGTAGAGCCTTTA
AAAGAGCAATTGGAACGTAAACCAAAGGCGTTTCCAAAATTAAAAATTAACCGAGAGGTC
GCCAACATTGATGACTTTAAATTCGAAGATTTTGAGTTAATTGGTTACGATCCTTACCCC
ACAATAAAAATGGAAATGGCTGTTTAATTATTAAATATATAACAAAAAGCCTAAAGAGAA
TAAACGAGTTTCATAGCTCTTTAAAAATTATAATTTTTATATACATACTTATAAAAGCCA
TACGAGACTTTATGTCAACATCCTATGGCTTCTACTTCTGCAGCAATA
>g11955.t2 Gene=g11955 Length=251
MRFNLRDQFPLLTTKRVFWRGLVEELLWFIQGSTDAKLLQAKNVRIWDGNSTREFLDASG
FHDRQVGDLGPVYGFQWRHYSAEYKTCNDDYTGKGIDQLKDVIERIKTNPNDRRIIMTAW
NPVDIPKMALPPCHCLVQFYVANGELSCQLYQRSADIGLGVPFNIASYALLTYMIAHVTN
LKPGDFVHSLGDTHVYLNHVEPLKEQLERKPKAFPKLKINREVANIDDFKFEDFELIGYD
PYPTIKMEMAV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11955.t2 | CDD | cd00351 | TS_Pyrimidine_HMase | 1 | 204 | 5.63345E-105 |
| 11 | g11955.t2 | Gene3D | G3DSA:3.30.572.10 | Thymidylate Synthase | 1 | 251 | 2.6E-126 |
| 4 | g11955.t2 | Hamap | MF_00008 | Thymidylate synthase [thyA]. | 1 | 251 | 30.065117 |
| 2 | g11955.t2 | PANTHER | PTHR11548 | THYMIDYLATE SYNTHASE 1 | 1 | 251 | 5.5E-154 |
| 3 | g11955.t2 | PANTHER | PTHR11548:SF2 | THYMIDYLATE SYNTHASE | 1 | 251 | 5.5E-154 |
| 6 | g11955.t2 | PRINTS | PR00108 | Thymidylate synthase family signature | 9 | 30 | 2.7E-54 |
| 8 | g11955.t2 | PRINTS | PR00108 | Thymidylate synthase family signature | 102 | 121 | 2.7E-54 |
| 7 | g11955.t2 | PRINTS | PR00108 | Thymidylate synthase family signature | 128 | 143 | 2.7E-54 |
| 9 | g11955.t2 | PRINTS | PR00108 | Thymidylate synthase family signature | 146 | 172 | 2.7E-54 |
| 5 | g11955.t2 | PRINTS | PR00108 | Thymidylate synthase family signature | 184 | 201 | 2.7E-54 |
| 1 | g11955.t2 | Pfam | PF00303 | Thymidylate synthase | 1 | 251 | 1.2E-105 |
| 13 | g11955.t2 | ProSitePatterns | PS00091 | Thymidylate synthase active site. | 113 | 141 | - |
| 10 | g11955.t2 | SUPERFAMILY | SSF55831 | Thymidylate synthase/dCMP hydroxymethylase | 1 | 251 | 7.85E-125 |
| 14 | g11955.t2 | TIGRFAM | TIGR03284 | thym_sym: thymidylate synthase | 1 | 251 | 5.9E-100 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
