General information for g13878.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 7.
Parent gene
- The parent gene g13878 is located on chr_1: 33088389..33089650 (- 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 | g13878 | g13878.t1 | TTS | g13878.t1 | 33088289 | 33088289 |
| chr_1 | g13878 | g13878.t1 | isoform | g13878.t1 | 33088389 | 33089650 |
| chr_1 | g13878 | g13878.t1 | exon | g13878.t1.exon1 | 33088389 | 33089180 |
| chr_1 | g13878 | g13878.t1 | cds | g13878.t1.CDS1 | 33088389 | 33089180 |
| chr_1 | g13878 | g13878.t1 | exon | g13878.t1.exon2 | 33089245 | 33089493 |
| chr_1 | g13878 | g13878.t1 | cds | g13878.t1.CDS2 | 33089245 | 33089493 |
| chr_1 | g13878 | g13878.t1 | exon | g13878.t1.exon3 | 33089552 | 33089650 |
| chr_1 | g13878 | g13878.t1 | cds | g13878.t1.CDS3 | 33089552 | 33089650 |
| chr_1 | g13878 | g13878.t1 | TSS | g13878.t1 | 33089714 | 33089714 |
Sequences
>g13878.t1 Gene=g13878 Length=1140
ATGGCACCTGAAAAGCCACAAAAAAGTGATTCAAGACGTGAAGAAGTTGATTTAGAGACG
CAATTCATTCTTAGATTACCCGAGGAATATGCTGGAAAACTTAGAGAAGCTATTAGATCT
GGAGCACAAAACATAAAAGAACGTCTTGCTATTTCCTTAGAAAATGATTTAAGAAAAGGA
ATGGTTCGAATGGACGATCGATATTTATATGCAAAAGTTGTTGATTTACCTTGTATAATT
GAATCTCATAAAACAATTGATAAGAAATCATTTTATAAAACTGCTGATATATGTCAAATG
GTAGTATGCAAAGAAGAGCCTGATCCTGTCACCGATGATGAATCACCAGTGAAAAATAAG
AAGAAAGATCCAAACAAAGTTGATAAAAAATTTTTGTATCCACATGGCATAACTCCCTCA
TTAAAAAATGTTCGTAAAAGAAGATTTAGAAAAACACTGAAAAAGAAGAATGTTGAGTTG
CCTGAAATTGAGAAAGAAGTAAAGCGACTGTTGAGAACAGATAATGAAGCAGTGAGTGTG
AAGTGGGAAATTATTGAAAGTGAAGAGCCAATGGAACCTGAGCAAGGTCGAGAATCGCCA
GTTAAAAGTAAAAAGCAAAGTGGTGCTAAAGGTAGAGAAGCAAAAAGCAAGAAAGAAACA
TTACCTGTTGATGAACATCACATTTTCGGTGAAGAGGTGTCAGATTCAGAAGAAGAGGAC
ATAAATGTGAATGAAACAGTACCCGATTTAGATATTGATGAAGATTCTAGAAGTCGTTTC
AGTGATTCAAATTCAATGATGCAAGGACTTCAATCGGCATCAAACAGTCAAATGATGGGC
GATTTCAGCAAGACTGAATTCAGTTCATCGATGTTTGAGGATGACGCTGGTGCAGGAACT
AGCTCACAACATATGGAAGAAGAAGAATCAATGGACTTTATGACAGCAAAAGAAAACTCA
AGAGCAAGTTCATTACGTCGTGAACTGCAAGAACTAAAAGTTAGTCAATCTCAGATTGAG
CAAGAAATTCAAACAATTGACAATAAGAAGCTTAAAGAGCGGCTTCAAGAAGATCTCGAG
AACATTATGGGTAAAATAATAATGAAACAACTTGAGCTTCAAGAATTTGAAGACCAGTAA
>g13878.t1 Gene=g13878 Length=379
MAPEKPQKSDSRREEVDLETQFILRLPEEYAGKLREAIRSGAQNIKERLAISLENDLRKG
MVRMDDRYLYAKVVDLPCIIESHKTIDKKSFYKTADICQMVVCKEEPDPVTDDESPVKNK
KKDPNKVDKKFLYPHGITPSLKNVRKRRFRKTLKKKNVELPEIEKEVKRLLRTDNEAVSV
KWEIIESEEPMEPEQGRESPVKSKKQSGAKGREAKSKKETLPVDEHHIFGEEVSDSEEED
INVNETVPDLDIDEDSRSRFSDSNSMMQGLQSASNSQMMGDFSKTEFSSSMFEDDAGAGT
SSQHMEEEESMDFMTAKENSRASSLRRELQELKVSQSQIEQEIQTIDNKKLKERLQEDLE
NIMGKIIMKQLELQEFEDQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g13878.t1 | CDD | cd08047 | TAF7 | 19 | 185 | 6.04533E-65 |
| 11 | g13878.t1 | Coils | Coil | Coil | 153 | 173 | - |
| 10 | g13878.t1 | Coils | Coil | Coil | 322 | 349 | - |
| 5 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 233 | - |
| 7 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 189 | 278 | - |
| 9 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 234 | 249 | - |
| 6 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 278 | - |
| 4 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 294 | 324 | - |
| 8 | g13878.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 300 | 324 | - |
| 2 | g13878.t1 | PANTHER | PTHR12228 | TRANSCRIPTION INITIATION FACTOR TFIID 55 KD SUBUNIT-RELATED | 13 | 378 | 2.7E-64 |
| 1 | g13878.t1 | Pfam | PF04658 | TAFII55 protein conserved region | 18 | 177 | 1.2E-60 |
| 3 | g13878.t1 | SMART | SM01370 | TAFII55_N_2 | 18 | 179 | 5.6E-84 |
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:0006367 | transcription initiation from RNA polymerase II promoter | BP |
| GO:0005669 | transcription factor TFIID complex | CC |
KEGG
Orthology
- This transcript has been annotated with K03132 (transcription initiation factor TFIID subunit 7)
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.
