Gene loci information

Transcript annotation

  • This transcript has been annotated as Transketolase-like protein 2.

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 g11672 g11672.t1 TTS g11672.t1 17734070 17734070
chr_1 g11672 g11672.t1 isoform g11672.t1 17734286 17737163
chr_1 g11672 g11672.t1 exon g11672.t1.exon1 17734286 17735931
chr_1 g11672 g11672.t1 cds g11672.t1.CDS1 17734286 17735931
chr_1 g11672 g11672.t1 exon g11672.t1.exon2 17736008 17736135
chr_1 g11672 g11672.t1 cds g11672.t1.CDS2 17736008 17736135
chr_1 g11672 g11672.t1 exon g11672.t1.exon3 17737063 17737163
chr_1 g11672 g11672.t1 cds g11672.t1.CDS3 17737063 17737163
chr_1 g11672 g11672.t1 TSS g11672.t1 17737269 17737269

Sequences

>g11672.t1 Gene=g11672 Length=1875
ATGTATCGTAAACCAGAAGCTGCAAAAATTCAAGAATTAAAAGACATTGCTCATCGATTG
AGAATCCACTCAATTACAAGCACAGAACAATCGAAATCAGGACATCCAACATCATGTGCA
TCGATTGCAGAAATTCTCTCAGTCTTATTTTTCAATTCTATGCGTTATAAAATAAGTGCA
CCACGTGATGCAGCAGCAGACCGTTTTGTTCTATCAAAGGGTCATGCAGCTCCAATATTG
TATGCTGCATGGGCTGAAGCTGGTCTTTTTCCAATAAGTGAATTGCAAAATTTGCGTAAA
ATAGATTCTGATTTAGAAGGACACCCAACTCCACGCTTACCATTTATTGACGTTGGAACG
GGATCATTAGGTCAAGGTCTTTCGATTGGCGCTGGAATGGCATACGTTGGAAAAAATTAT
GATAAAGCGAGTTATAGAACTTATGTACTCGTCGGAGATGGAGAATCTGCTGAAGGCTCG
ATATGGGAAGCTTTACATTTTGCTGGTCATTACAAATTAGATAATTTGTGTGTGATTTTT
GATGTCAATCGTTTAGGACAATCAGAACCAACATCTTTACAACATCAAATGGAAACATAT
CGTAAACGTTTGGATGCTTTTGGATTAAATGCCATTGTTGTCGATGGACATGACGTTGAA
GAACTTTGTCGTGCATTTTACGAAGCAGAGCAAACAAAAGGTCGACCAACTGCTATAATT
GCAAAGACATTTAAGGGTAAATATTTCCCAAATATTGAAGATCTCGAGAACTGGCATGGA
AAACCATTAGGTGCCAATGCTGAAGCTGTAATCAAGCATTTGGAAAGTCTTATTAAAAAC
AAAGGCGCATTGACTTTACAAGCTCAATCTCCTCTAGATGAGCCACCAACTGTTTCATTG
TCTGATGTTACACTTTCATCGCCACCTGCTTATAAACTAGGAGAACAAGTTGCTACTCGT
CTTGCATATGGAACAGCTTTGGCAAAAATTGGAGCTTCTAATGATCGCGTTATTGCTCTA
GATGGTGACACTAAAAATTCAACTTATTCTGAAAAATTAAAAAAAGCATTTCCTGAACGC
TATATCGAATGTTTCATTGCCGAACAGAATCTCGTTGGAGTTGCAGTTGGCACTGCCTGT
CGTGATCGTACAATAGCATTTGTATCAACATTTGCAACATTCTTTACAAGAGCATTCGAT
CAAATCAGAATGGCTGCAATCAGTCAATCTAACGTCAACTTTGTTGGTTCACATTGTGGT
GTATCAATCGGAGAAGATGGTCCATCTCAAATGGGATTGGAAGATCTTGCTTTATTCCGT
TCGATTCCTGGTTCAACTGTTTTTTATCCATCAGATGCTGTCTCTACAGAGCGTGCTGTT
GAGCTTGCAGCAAACACTAAAGGCATTTGCTATATTCGTACATCTCGTCCAAATACTGAG
GTCATTTATGCAAACGATGCTTCATTGCAAATTGGAAAGGCACGAGTCATTAAACATTCT
GCTAATGATCAAGTTTTACTTATTGGCGCATGTGTAACATTATATGAATCCCTAAAGGCA
GCAAAAGAATTAGAAGGACTTGGTGTAAATGCACGCGTTTTAGATCCATTTACTATCAAG
CCTATTGATCGTGATGGAATAATTGCTAATGCACAAGAATGTGGAGGCCGAATTGTTGTT
GTTGAGGATCATTATCGTGAAGGTGGTTTGGGAGAAGCAGTGCTCTCAGCAGTTGCAGAT
CAACGAAATATTGTTGTCAAGCATCTCTTCGTTCCAACAGTACCTCGTTCAGGTCCACCA
GCTGTTTTGATTGATACATTTGGCATCAGTTCACGTCATATTATTGCAGCCGCACAAGAC
ATTTTAAAATTGTAA

>g11672.t1 Gene=g11672 Length=624
MYRKPEAAKIQELKDIAHRLRIHSITSTEQSKSGHPTSCASIAEILSVLFFNSMRYKISA
PRDAAADRFVLSKGHAAPILYAAWAEAGLFPISELQNLRKIDSDLEGHPTPRLPFIDVGT
GSLGQGLSIGAGMAYVGKNYDKASYRTYVLVGDGESAEGSIWEALHFAGHYKLDNLCVIF
DVNRLGQSEPTSLQHQMETYRKRLDAFGLNAIVVDGHDVEELCRAFYEAEQTKGRPTAII
AKTFKGKYFPNIEDLENWHGKPLGANAEAVIKHLESLIKNKGALTLQAQSPLDEPPTVSL
SDVTLSSPPAYKLGEQVATRLAYGTALAKIGASNDRVIALDGDTKNSTYSEKLKKAFPER
YIECFIAEQNLVGVAVGTACRDRTIAFVSTFATFFTRAFDQIRMAAISQSNVNFVGSHCG
VSIGEDGPSQMGLEDLALFRSIPGSTVFYPSDAVSTERAVELAANTKGICYIRTSRPNTE
VIYANDASLQIGKARVIKHSANDQVLLIGACVTLYESLKAAKELEGLGVNARVLDPFTIK
PIDRDGIIANAQECGGRIVVVEDHYREGGLGEAVLSAVADQRNIVVKHLFVPTVPRSGPP
AVLIDTFGISSRHIIAAAQDILKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g11672.t1 CDD cd02012 TPP_TK 19 265 1.67123E-133
15 g11672.t1 CDD cd07033 TPP_PYR_DXS_TK_like 322 476 1.5881E-69
11 g11672.t1 Gene3D G3DSA:3.40.50.970 - 1 296 2.7E-101
12 g11672.t1 Gene3D G3DSA:3.40.50.970 - 298 491 2.5E-70
13 g11672.t1 Gene3D G3DSA:3.40.50.920 - 492 624 7.3E-36
4 g11672.t1 PANTHER PTHR43195 TRANSKETOLASE 3 622 0.0
5 g11672.t1 PANTHER PTHR43195:SF1 FI06132P-RELATED 3 622 0.0
3 g11672.t1 Pfam PF00456 Transketolase, thiamine diphosphate binding domain 15 271 4.6E-45
2 g11672.t1 Pfam PF02779 Transketolase, pyrimidine binding domain 316 479 4.2E-40
1 g11672.t1 Pfam PF02780 Transketolase, C-terminal domain 493 614 1.6E-26
10 g11672.t1 ProSitePatterns PS00802 Transketolase signature 2. 424 440 -
9 g11672.t1 SMART SM00861 Transket_pyr_3 317 481 2.6E-49
7 g11672.t1 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding) 9 275 4.72E-86
6 g11672.t1 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding) 303 482 1.55E-55
8 g11672.t1 SUPERFAMILY SSF52922 TK C-terminal domain-like 489 623 1.05E-24

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:0003824 catalytic 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