Gene loci information

Transcript annotation

  • This transcript has been annotated as Thymidylate synthase.

Parent gene

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.t9 TTS g11955.t9 19785579 19785579
chr_1 g11955 g11955.t9 isoform g11955.t9 19785720 19787708
chr_1 g11955 g11955.t9 exon g11955.t9.exon1 19785720 19786507
chr_1 g11955 g11955.t9 cds g11955.t9.CDS1 19785720 19786507
chr_1 g11955 g11955.t9 exon g11955.t9.exon2 19786580 19786769
chr_1 g11955 g11955.t9 cds g11955.t9.CDS2 19786580 19786769
chr_1 g11955 g11955.t9 exon g11955.t9.exon3 19786827 19786859
chr_1 g11955 g11955.t9 cds g11955.t9.CDS3 19786827 19786829
chr_1 g11955 g11955.t9 exon g11955.t9.exon4 19787679 19787708
chr_1 g11955 g11955.t9 TSS g11955.t9 19787708 19787708

Sequences

>g11955.t9 Gene=g11955 Length=1041
CTCTTTCGTTTACATTTTCTCATTTTAACAAATCCTGATTTCATTCATAAAATTGATAAA
ATGGAGAATACAGATAATGGAAATTTAACAAATAATTCAACAGAAAACATTCAAAAACTT
AAAGTAAATCAAAAAGTCAATGGATCTCATAATCAGGAAAATTTTGAAGAGGAGATAGAA
CATGATGAAGTGCAGTATTTAAATTTAATTCGCAATGTACTGAAACGTGGAATAATTCGT
GGAGATAGAACTGGTGTTGGTACAATCAGTATTTTCGGTGCACAAATGAGATTTAATTTG
CGAGATCAATTTCCTTTGCTAACAACTAAAAGAGTTTTTTGGCGAGGACTTGTTGAAGAA
TTGCTCTGGTTTATTCAAGGTTCAACAGATGCAAAGCTGTTACAAGCGAAAAACGTTCGA
ATTTGGGATGGTAATAGTACCCGAGAGTTTCTCGATGCATCTGGATTTCATGATCGTCAA
GTTGGTGATTTAGGTCCTGTCTATGGTTTTCAATGGCGGCATTATAGTGCTGAATATAAA
ACTTGTAATGACGATTATACTGGTAAAGGTATTGATCAATTAAAAGATGTTATCGAGCGT
ATTAAAACAAATCCAAATGATCGTCGCATTATAATGACTGCATGGAATCCAGTTGATATT
CCAAAGATGGCTCTTCCACCATGTCATTGTCTTGTCCAGTTTTACGTTGCTAACGGTGAA
TTGAGTTGTCAATTGTACCAAAGAAGTGCCGATATCGGTCTCGGAGTTCCTTTCAATATA
GCATCATATGCACTCTTGACCTATATGATTGCTCATGTCACAAACTTGAAACCAGGTGAT
TTTGTTCATTCTTTAGGTGATACACATGTTTATCTTAATCACGTAGAGCCTTTAAAAGAG
CAATTGGAACGTAAACCAAAGGCGTTTCCAAAATTAAAAATTAACCGAGAGGTCGCCAAC
ATTGATGACTTTAAATTCGAAGATTTTGAGTTAATTGGTTACGATCCTTACCCCACAATA
AAAATGGAAATGGCTGTTTAA

>g11955.t9 Gene=g11955 Length=326
MENTDNGNLTNNSTENIQKLKVNQKVNGSHNQENFEEEIEHDEVQYLNLIRNVLKRGIIR
GDRTGVGTISIFGAQMRFNLRDQFPLLTTKRVFWRGLVEELLWFIQGSTDAKLLQAKNVR
IWDGNSTREFLDASGFHDRQVGDLGPVYGFQWRHYSAEYKTCNDDYTGKGIDQLKDVIER
IKTNPNDRRIIMTAWNPVDIPKMALPPCHCLVQFYVANGELSCQLYQRSADIGLGVPFNI
ASYALLTYMIAHVTNLKPGDFVHSLGDTHVYLNHVEPLKEQLERKPKAFPKLKINREVAN
IDDFKFEDFELIGYDPYPTIKMEMAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11955.t9 CDD cd00351 TS_Pyrimidine_HMase 45 279 1.82607E-119
11 g11955.t9 Gene3D G3DSA:3.30.572.10 Thymidylate Synthase 25 326 3.2E-143
4 g11955.t9 Hamap MF_00008 Thymidylate synthase [thyA]. 43 326 38.059769
2 g11955.t9 PANTHER PTHR11548 THYMIDYLATE SYNTHASE 1 22 326 2.1E-172
3 g11955.t9 PANTHER PTHR11548:SF2 THYMIDYLATE SYNTHASE 22 326 2.1E-172
6 g11955.t9 PRINTS PR00108 Thymidylate synthase family signature 84 105 6.1E-54
5 g11955.t9 PRINTS PR00108 Thymidylate synthase family signature 177 196 6.1E-54
7 g11955.t9 PRINTS PR00108 Thymidylate synthase family signature 203 218 6.1E-54
9 g11955.t9 PRINTS PR00108 Thymidylate synthase family signature 221 247 6.1E-54
8 g11955.t9 PRINTS PR00108 Thymidylate synthase family signature 259 276 6.1E-54
1 g11955.t9 Pfam PF00303 Thymidylate synthase 45 326 5.3E-119
13 g11955.t9 ProSitePatterns PS00091 Thymidylate synthase active site. 188 216 -
10 g11955.t9 SUPERFAMILY SSF55831 Thymidylate synthase/dCMP hydroxymethylase 37 326 5.76E-141
14 g11955.t9 TIGRFAM TIGR03284 thym_sym: thymidylate synthase 45 326 7.3E-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

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.

Raw TPM values