Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 1.

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_3 g545 g545.t33 isoform g545.t33 4002413 4003633
chr_3 g545 g545.t33 exon g545.t33.exon1 4002413 4003633
chr_3 g545 g545.t33 cds g545.t33.CDS1 4002413 4002928
chr_3 g545 g545.t33 TTS g545.t33 4002418 4002418
chr_3 g545 g545.t33 TSS g545.t33 4003621 4003621

Sequences

>g545.t33 Gene=g545 Length=1221
AGTTAGGTAGTGGCGAATACAAAATTATTTTGACTTGATAGCATCAATTTCGTAAATTTT
TTAATAATTTGATTTTGCACAGTAAATACTTTTTAAAAGTGAGAAAACTGTAAATAAAGA
CTTAGATAAGAATTAATTTTATTTAATAGACATCAAGGTGAGTTATTTTCATACAAATTT
TATAACTAAATTTATAAAATATAAATTTTTGTAGCTGATAAGATGTCAAACATTGATTCT
GAAGAGGAACATGATGATGATGCATTGAATAAGCAATTAACTGGTTTTTTATTTGGTAAT
ATTGATGAAGATGGCAAGTTAGAGTCAGATTTCCTAGATGAGGACGTTAAAAAACATGTT
GCATCTCTTTCAAAGTAAATATAAACAAACATCCAGTTGAGAATTTTATTAATTTTCATT
TGTCCTAATAGATTTGGACTTTACAATCTTATTGGATCTGGATTTGTATCAGATGATGAG
GCAAGTGATTCAGATTCGGATTCTTCAGATTCAGGCGCTGAAAAAGCAACTAAAAGAAGA
CGACTTTCTACACCGACAGATTATAAAATTAAAGAAGAGTCAGCAGAAGATTTCTTTGAT
ATAAATGAATTAGCTGATGAGCCACCACCAAAAATATATGATCCAAAAGATGATTATGAT
ATCGAAGATGCTATTCCTGCCGCAAAAGTTGTTGCTGCTGATGGAATGCAAGTTGATGGA
AGTTCTGATTCAAATAAAAATGGCTCATCAGATGATAAACAATTAATGCCACCTCCACCT
CTTGAAGCTGCTCCATCAGTAAAACAAGATGAAAGTAATTCAAATACAGAAACTACAGTA
AATGGAACAACTGAAAAGAAAACAGATGGCAAAAAATTAGAAACTCCTCTTGGTGCAATG
CTTCCATCTAAATATGCAAATGTTGATGTCACTGAACTATTTCCAGACTTTCGACAAGAC
AAAGTTTTACGATTTTCACGTCTTTTTGGTCCAGGCAAATTTTCAAGTCTCCCACAAATT
TGGCGAAGTGTTCGTCGCAAAGCTAAGAAACGAAGAAAAGAGCGTGAGAAGCTTACATCA
GAATCTAATACAAGTGATTCAGATGCAGATTCTAGAAGATTTGTTGGATTTAATTTGAGA
TTTGCTCCGACACCACCAAGAGAATTGATAGCATCTGACGATGAAGATAAATTATTAAGT
GAAAAAACAAATGAAGAAAAA

>g545.t33 Gene=g545 Length=172
MQVDGSSDSNKNGSSDDKQLMPPPPLEAAPSVKQDESNSNTETTVNGTTEKKTDGKKLET
PLGAMLPSKYANVDVTELFPDFRQDKVLRFSRLFGPGKFSSLPQIWRSVRRKAKKRRKER
EKLTSESNTSDSDADSRRFVGFNLRFAPTPPRELIASDDEDKLLSEKTNEEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g545.t33 Coils Coil Coil 163 172 -
7 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 1 60 -
9 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 1 17 -
8 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 32 48 -
4 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 110 134 -
6 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 119 133 -
5 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 150 172 -
3 g545.t33 MobiDBLite mobidb-lite consensus disorder prediction 154 172 -
1 g545.t33 PANTHER PTHR13900:SF1 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 1 36 163 1.4E-17
2 g545.t33 PANTHER PTHR13900 TRANSCRIPTION INITIATION FACTOR TFIID 36 163 1.4E-17

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g545/g545.t33; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g545.t33.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

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