General information for g13899.t5
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 13.
Parent gene
- The parent gene g13899 is located on chr_1: 33201281..33201855 (- 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_1 | g13899 | g13899.t5 | isoform | g13899.t5 | 33200945 | 33201855 |
| chr_1 | g13899 | g13899.t5 | exon | g13899.t5.exon1 | 33200945 | 33201429 |
| chr_1 | g13899 | g13899.t5 | TTS | g13899.t5 | 33200961 | 33200961 |
| chr_1 | g13899 | g13899.t5 | cds | g13899.t5.CDS1 | 33201281 | 33201429 |
| chr_1 | g13899 | g13899.t5 | exon | g13899.t5.exon2 | 33201560 | 33201758 |
| chr_1 | g13899 | g13899.t5 | cds | g13899.t5.CDS2 | 33201560 | 33201758 |
| chr_1 | g13899 | g13899.t5 | exon | g13899.t5.exon3 | 33201814 | 33201855 |
| chr_1 | g13899 | g13899.t5 | cds | g13899.t5.CDS3 | 33201814 | 33201855 |
| chr_1 | g13899 | g13899.t5 | TSS | g13899.t5 | 33202700 | 33202700 |
Sequences
>g13899.t5 Gene=g13899 Length=726
ATGACAACATTACCAGCCGAGGAAATTTTTGATCAACCTGAATTTGATGAAGAAGAAACT
CCTGAAGATTTTAATGAAGCTACTGGTCGTAAAAGATTATTTAGTAAGGAATTAAGATGT
ATGATGTATGGCTTCGGTGATGATCAGAATCCATTTACTGAAAGTGTTGATTTATTAGAA
GACCTTGTGATTGAATTCATAACAGAAATCACACATAAGGCAAGCGAAATAGGCAAAACA
GGAAATTTAAAATTTGTAGAAGACATTGTGTTTTTAGTAAGAAAAGATCAACGAAAATAT
GCTCGTGTAAAGGACTTATTAACCATGAATGAAGAATTAAAGAAAGCAAGAAAAGCCTTT
GATGAAGTAAAATATGTGTCAACATCATAAATCTATTAGTAAAATATTCTTTATTTGATT
TTCTCTCACTTATATTCTTAAATCAAGTTTTTACGAAAAAGCTGTATATAATAATAATGA
AATTTAGATCAAGTAGAATTAATATAAAGGAATGTGTTCTCAAAATACATGGAAGTGATC
AAGAGTCATCATCCATTACAACGTCTCCCTCTTCATTATCTTCTTCTATATCTATTTCAA
CTCCTTTGATAAGTTTTGAGATAATTTGCACTGTCGTTTTCGAATTATCAGAAATGTTCA
AACCAAATCTAAGAAAAAGAACTCATAAATAAATTAAAAAGAAAATAATGCATAGAAAAA
CTTACT
>g13899.t5 Gene=g13899 Length=129
MTTLPAEEIFDQPEFDEEETPEDFNEATGRKRLFSKELRCMMYGFGDDQNPFTESVDLLE
DLVIEFITEITHKASEIGKTGNLKFVEDIVFLVRKDQRKYARVKDLLTMNEELKKARKAF
DEVKYVSTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13899.t5 | CDD | cd07978 | TAF13 | 31 | 121 | 2.24459E-40 |
| 6 | g13899.t5 | Gene3D | G3DSA:1.10.20.10 | Histone | 33 | 77 | 2.4E-25 |
| 5 | g13899.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 26 | - |
| 2 | g13899.t5 | PANTHER | PTHR11380:SF13 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 13 | 9 | 126 | 3.0E-54 |
| 3 | g13899.t5 | PANTHER | PTHR11380 | TRANSCRIPTION INITIATION FACTOR TFIID/SUPT3-RELATED | 9 | 126 | 3.0E-54 |
| 1 | g13899.t5 | Pfam | PF02269 | Transcription initiation factor IID, 18kD subunit | 33 | 122 | 7.0E-34 |
| 4 | g13899.t5 | SUPERFAMILY | SSF47113 | Histone-fold | 34 | 76 | 6.49E-13 |
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:0046982 | protein heterodimerization activity | MF |
| GO:0006366 | transcription by RNA polymerase II | BP |
KEGG
Orthology
- This transcript has been annotated with K03127 (transcription initiation factor TFIID subunit 13)
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.
