General information for g545.t34
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 1.
Parent gene
- The parent gene g545 is located on chr_3: 4002413..4003652 (- 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_3 | g545 | g545.t34 | isoform | g545.t34 | 4002413 | 4003652 |
| chr_3 | g545 | g545.t34 | exon | g545.t34.exon1 | 4002413 | 4003202 |
| chr_3 | g545 | g545.t34 | cds | g545.t34.CDS1 | 4002413 | 4003202 |
| chr_3 | g545 | g545.t34 | TTS | g545.t34 | 4002418 | 4002418 |
| chr_3 | g545 | g545.t34 | exon | g545.t34.exon2 | 4003260 | 4003419 |
| chr_3 | g545 | g545.t34 | cds | g545.t34.CDS2 | 4003260 | 4003411 |
| chr_3 | g545 | g545.t34 | exon | g545.t34.exon3 | 4003477 | 4003652 |
| chr_3 | g545 | g545.t34 | TSS | g545.t34 | 4003621 | 4003621 |
Sequences
>g545.t34 Gene=g545 Length=1126
ATGAAAGAATTACGACACAAGTTAGGTAGTGGCGAATACAAAATTATTTTGACTTGATAG
CATCAATTTCGTAAATTTTTTAATAATTTGATTTTGCACAGTAAATACTTTTTAAAAGTG
AGAAAACTGTAAATAAAGACTTAGATAAGAATTAATTTTATTTAATAGACATCAAGCTGA
TAAGATGTCAAACATTGATTCTGAAGAGGAACATGATGATGATGCATTGAATAAGCAATT
AACTGGTTTTTTATTTGGTAATATTGATGAAGATGGCAAGTTAGAGTCAGATTTCCTAGA
TGAGGACGTTAAAAAACATGTTGCATCTCTTTCAAAATTTGGACTTTACAATCTTATTGG
ATCTGGATTTGTATCAGATGATGAGGCAAGTGATTCAGATTCGGATTCTTCAGATTCAGG
CGCTGAAAAAGCAACTAAAAGAAGACGACTTTCTACACCGACAGATTATAAAATTAAAGA
AGAGTCAGCAGAAGATTTCTTTGATATAAATGAATTAGCTGATGAGCCACCACCAAAAAT
ATATGATCCAAAAGATGATTATGATATCGAAGATGCTATTCCTGCCGCAAAAGTTGTTGC
TGCTGATGGAATGCAAGTTGATGGAAGTTCTGATTCAAATAAAAATGGCTCATCAGATGA
TAAACAATTAATGCCACCTCCACCTCTTGAAGCTGCTCCATCAGTAAAACAAGATGAAAG
TAATTCAAATACAGAAACTACAGTAAATGGAACAACTGAAAAGAAAACAGATGGCAAAAA
ATTAGAAACTCCTCTTGGTGCAATGCTTCCATCTAAATATGCAAATGTTGATGTCACTGA
ACTATTTCCAGACTTTCGACAAGACAAAGTTTTACGATTTTCACGTCTTTTTGGTCCAGG
CAAATTTTCAAGTCTCCCACAAATTTGGCGAAGTGTTCGTCGCAAAGCTAAGAAACGAAG
AAAAGAGCGTGAGAAGCTTACATCAGAATCTAATACAAGTGATTCAGATGCAGATTCTAG
AAGATTTGTTGGATTTAATTTGAGATTTGCTCCGACACCACCAAGAGAATTGATAGCATC
TGACGATGAAGATAAATTATTAAGTGAAAAAACAAATGAAGAAAAA
>g545.t34 Gene=g545 Length=314
MSNIDSEEEHDDDALNKQLTGFLFGNIDEDGKLESDFLDEDVKKHVASLSKFGLYNLIGS
GFVSDDEASDSDSDSSDSGAEKATKRRRLSTPTDYKIKEESAEDFFDINELADEPPPKIY
DPKDDYDIEDAIPAAKVVAADGMQVDGSSDSNKNGSSDDKQLMPPPPLEAAPSVKQDESN
SNTETTVNGTTEKKTDGKKLETPLGAMLPSKYANVDVTELFPDFRQDKVLRFSRLFGPGK
FSSLPQIWRSVRRKAKKRRKEREKLTSESNTSDSDADSRRFVGFNLRFAPTPPRELIASD
DEDKLLSEKTNEEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g545.t34 | Gene3D | G3DSA:1.10.1100.10 | - | 14 | 68 | 1.5E-9 |
| 9 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 65 | 205 | - |
| 12 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 75 | 105 | - |
| 6 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 114 | 131 | - |
| 5 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 145 | 159 | - |
| 7 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 174 | 190 | - |
| 4 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 276 | - |
| 11 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 275 | - |
| 8 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 292 | 314 | - |
| 10 | g545.t34 | MobiDBLite | mobidb-lite | consensus disorder prediction | 296 | 314 | - |
| 2 | g545.t34 | PANTHER | PTHR13900 | TRANSCRIPTION INITIATION FACTOR TFIID | 5 | 312 | 3.2E-27 |
| 1 | g545.t34 | Pfam | PF09247 | TATA box-binding protein binding | 6 | 58 | 4.4E-17 |
| 3 | g545.t34 | SUPERFAMILY | SSF47055 | TAF(II)230 TBP-binding fragment | 15 | 59 | 1.01E-12 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g545/g545.t34; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g545.t34.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.
