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.t7 TTS g11955.t7 19785579 19785579
chr_1 g11955 g11955.t7 isoform g11955.t7 19785720 19787658
chr_1 g11955 g11955.t7 exon g11955.t7.exon1 19785720 19786507
chr_1 g11955 g11955.t7 cds g11955.t7.CDS1 19785720 19786475
chr_1 g11955 g11955.t7 exon g11955.t7.exon2 19786580 19786801
chr_1 g11955 g11955.t7 exon g11955.t7.exon3 19787494 19787658
chr_1 g11955 g11955.t7 TSS g11955.t7 19787708 19787708

Sequences

>g11955.t7 Gene=g11955 Length=1175
TGTTCATTTTTACAAAAATGATGATGTTTCAGATCAATGTATTCCATATACCAATCGATA
AAGCACATTAAAATGCATCGATTGGTCGAGGGAATAGTGATTTAATTGCGTATTTATCGA
GATATTTCATCTCAAAGTCGCCATTTTTTTGTTTACATTTTCATTTATAATTTATTATCA
TTAAAAATTTTTGGCAGGAGAATACAGATAATGGAAATTTAACAAATAATTCAACAGAAA
ACATTCAAAAACTTAAAGTAAATCAAAAAGTCAATGGATCTCATAATCAGGAAAATTTTG
AAGAGGAGATAGAACATGATGAAGTGCAGTATTTAAATTTAATTCGCAATGTACTGAAAC
GTGGAATAATTCGTGGAGATAGAACTGGTGTTGGTACAATCAGTATTTTCGGTGCACAAA
TGAGATTTAATTTGCGAGATCAATTTCCTTTGCTAACAACTAAAAGAGTTTTTTGGCGAG
GACTTGTTGAAGAATTGCTCTGGTTTATTCAAGGTTCAACAGATGCAAAGCTGTTACAAG
CGAAAAACGTTCGAATTTGGGATGGTAATAGTACCCGAGAGTTTCTCGATGCATCTGGAT
TTCATGATCGTCAAGTTGGTGATTTAGGTCCTGTCTATGGTTTTCAATGGCGGCATTATA
GTGCTGAATATAAAACTTGTAATGACGATTATACTGGTAAAGGTATTGATCAATTAAAAG
ATGTTATCGAGCGTATTAAAACAAATCCAAATGATCGTCGCATTATAATGACTGCATGGA
ATCCAGTTGATATTCCAAAGATGGCTCTTCCACCATGTCATTGTCTTGTCCAGTTTTACG
TTGCTAACGGTGAATTGAGTTGTCAATTGTACCAAAGAAGTGCCGATATCGGTCTCGGAG
TTCCTTTCAATATAGCATCATATGCACTCTTGACCTATATGATTGCTCATGTCACAAACT
TGAAACCAGGTGATTTTGTTCATTCTTTAGGTGATACACATGTTTATCTTAATCACGTAG
AGCCTTTAAAAGAGCAATTGGAACGTAAACCAAAGGCGTTTCCAAAATTAAAAATTAACC
GAGAGGTCGCCAACATTGATGACTTTAAATTCGAAGATTTTGAGTTAATTGGTTACGATC
CTTACCCCACAATAAAAATGGAAATGGCTGTTTAA

>g11955.t7 Gene=g11955 Length=251
MRFNLRDQFPLLTTKRVFWRGLVEELLWFIQGSTDAKLLQAKNVRIWDGNSTREFLDASG
FHDRQVGDLGPVYGFQWRHYSAEYKTCNDDYTGKGIDQLKDVIERIKTNPNDRRIIMTAW
NPVDIPKMALPPCHCLVQFYVANGELSCQLYQRSADIGLGVPFNIASYALLTYMIAHVTN
LKPGDFVHSLGDTHVYLNHVEPLKEQLERKPKAFPKLKINREVANIDDFKFEDFELIGYD
PYPTIKMEMAV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11955.t7 CDD cd00351 TS_Pyrimidine_HMase 1 204 5.63345E-105
11 g11955.t7 Gene3D G3DSA:3.30.572.10 Thymidylate Synthase 1 251 2.6E-126
4 g11955.t7 Hamap MF_00008 Thymidylate synthase [thyA]. 1 251 30.065117
2 g11955.t7 PANTHER PTHR11548 THYMIDYLATE SYNTHASE 1 1 251 5.5E-154
3 g11955.t7 PANTHER PTHR11548:SF2 THYMIDYLATE SYNTHASE 1 251 5.5E-154
6 g11955.t7 PRINTS PR00108 Thymidylate synthase family signature 9 30 2.7E-54
8 g11955.t7 PRINTS PR00108 Thymidylate synthase family signature 102 121 2.7E-54
7 g11955.t7 PRINTS PR00108 Thymidylate synthase family signature 128 143 2.7E-54
9 g11955.t7 PRINTS PR00108 Thymidylate synthase family signature 146 172 2.7E-54
5 g11955.t7 PRINTS PR00108 Thymidylate synthase family signature 184 201 2.7E-54
1 g11955.t7 Pfam PF00303 Thymidylate synthase 1 251 1.2E-105
13 g11955.t7 ProSitePatterns PS00091 Thymidylate synthase active site. 113 141 -
10 g11955.t7 SUPERFAMILY SSF55831 Thymidylate synthase/dCMP hydroxymethylase 1 251 7.85E-125
14 g11955.t7 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.

Raw TPM values