General information for g10984.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transcription initiation factor TFIID subunit 6.
Parent gene
- The parent gene g10984 is located on chr_1: 13162876..13164132 (- 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 | g10984 | g10984.t3 | TTS | g10984.t3 | 13161806 | 13161806 |
| chr_1 | g10984 | g10984.t3 | isoform | g10984.t3 | 13161945 | 13164132 |
| chr_1 | g10984 | g10984.t3 | exon | g10984.t3.exon1 | 13161945 | 13162167 |
| chr_1 | g10984 | g10984.t3 | cds | g10984.t3.CDS1 | 13161945 | 13162167 |
| chr_1 | g10984 | g10984.t3 | exon | g10984.t3.exon2 | 13162234 | 13162802 |
| chr_1 | g10984 | g10984.t3 | cds | g10984.t3.CDS2 | 13162234 | 13162802 |
| chr_1 | g10984 | g10984.t3 | exon | g10984.t3.exon3 | 13162864 | 13163639 |
| chr_1 | g10984 | g10984.t3 | cds | g10984.t3.CDS3 | 13162864 | 13163639 |
| chr_1 | g10984 | g10984.t3 | exon | g10984.t3.exon4 | 13163702 | 13163978 |
| chr_1 | g10984 | g10984.t3 | cds | g10984.t3.CDS4 | 13163702 | 13163801 |
| chr_1 | g10984 | g10984.t3 | exon | g10984.t3.exon5 | 13164039 | 13164132 |
| chr_1 | g10984 | g10984.t3 | TSS | g10984.t3 | 13164809 | 13164809 |
Sequences
>g10984.t3 Gene=g10984 Length=1939
TTTTTTAAAATTCTAAAAATTAATATAAACAAATGATAATTATGAAGGAGTAGTGAGAGA
AAAGAGCTTGCTTTGAAAAGATTATATTTCAACTATATTCAAAAAAAATCTGATTGTTGT
TTTGAAAAAAATTCAAAAAATAACTTTTTTTAAAATTAATAAAATAGAGGAAACAAGTTA
AAAGTAAATACAAAAGTACCTGTATAGCGTAATTTAAAACTTTCAACATTGGATAAACTT
GAAAGCAAATAGAAATTTGAACGAATTTAGAATGGAAGACAAAATAAAGAATCCTGAAAT
AAATTCTCAGCATTTCGGCACAAACTTATCGCTTGAATCAATAAAAATTATTGCAGAATC
AATTGGAATTGGAAATTTATCAGATTCTGCTGCAAAAGAACTAAGTGATGATATTAGTTA
CAAATTAAAACAAATAGTGCAGGATGCTCAAAAATTTATGAATCATGCAAAAAGAACACG
CTTATCAATTGCTGATGTTGATCATTCATTGAAAATAAGAAATATTGAACCGCAGTATGG
ATTCATATGTAAAGAATTTATACCGTTTCGATTTGCTAGCGGTGGCGGTCGAGAACTTTA
CTTCCAAGAAGAGAAAGAAGTAGATTTGAATGATGTTATGACTTCAACAGCCCCAAAAGC
ACCTCTTGAAGTGACATTAAGAGCACATTGGCTTTGTGTTGATGGAATACAACCGACTAT
TCCAGAGAATCCTCCTCCTCTTTCAAAAGACGCTCAAATTCAAGATTCTGTAAATCCAAT
AAAGAAGATCGAGAAAGCTGATTTGAAAGATACAAGTGGAAAACCTGCCATTAAAGCACA
CAAGCTTAAAACTCATGAAACTGTGCATATCAAACAACTTGCACAGCATGAACTTTCAGT
GGAACAACAATTTTATTACAAAGAAATCACAGAAGCTTGTGTAGGTGCGGATGAGGCTCG
TCGTGCTGAAGCTCTTCAATCGCTTTGTTGTGATCCTGGAATACATGAAATGTTACCTAG
AATGTGTACATTCATTGCAGAAGGTGTCAAAATAAATGTAGTACAAAACAATCTAGCAAT
TTTGATTTACCTTATGCGTATGGTTCGAGCACTTTTGGACAATCCTGCACTTTTTCTTGA
AAAATATCTTCATGAATTAATTCCATCAGTTTCAACTTGCATTGTGTCAAAGCAATTGTG
CCAACGTCCAGAAGTTGATAATCATTGGGCTCTGAGAGATTTTGCTGCAAAATTAATGGC
GCAAATTTGTAAAAATTTCAACACATCGACAAATAATCTTCAAACACGTGTGACTCGTCT
TTTTAGCACTGCACTTCAAAATGACAAAGTTCCTTTATCATCTTTATATGGAGCAATTGA
GGGACTATCTGAGTTAGGTCATGAAGTGATCAAAGTATTTATAATTCCTCGATTGAAATT
CATTTCTGAAAGAGTGTGCAATATGCAAGCTACAGATATCAGCAATACAGAGAGAAATGC
GGCTGGACATATAAGAGCTTTGCTGGCAAAAGTTTGTGCACCAGTCTTAAAAACAATGAG
ACCATCACCAGATATCATTGAAGATTATAAGCGTGATTTTGGATTTTTGGGACCAGCATT
GCATCAAAGTGTTATGAAAGCACGTCAAACACCAAGTACTACACCTACAGCATCAACAGC
TTCATCAATATCGGTTCCATCTGTTACACCTCGAATAACATCAACACCTATTCAGCGTCA
AATTTCACAAAGTCAGCCAAGTCAAAAGTTTTTTGTTACAAAAGCAGCAAACTCACCATC
GACTTCATCAGGGAACATAGTCAAAATACAACAGAATAATCCACAAAAAATATTTATACA
AGCACCAAAAACAGTTTTTGTTGCTGCAAACACACAAGAACATGAACTTGAGATCGATGA
CTTATCGCATTTAGAATAA
>g10984.t3 Gene=g10984 Length=555
MEDKIKNPEINSQHFGTNLSLESIKIIAESIGIGNLSDSAAKELSDDISYKLKQIVQDAQ
KFMNHAKRTRLSIADVDHSLKIRNIEPQYGFICKEFIPFRFASGGGRELYFQEEKEVDLN
DVMTSTAPKAPLEVTLRAHWLCVDGIQPTIPENPPPLSKDAQIQDSVNPIKKIEKADLKD
TSGKPAIKAHKLKTHETVHIKQLAQHELSVEQQFYYKEITEACVGADEARRAEALQSLCC
DPGIHEMLPRMCTFIAEGVKINVVQNNLAILIYLMRMVRALLDNPALFLEKYLHELIPSV
STCIVSKQLCQRPEVDNHWALRDFAAKLMAQICKNFNTSTNNLQTRVTRLFSTALQNDKV
PLSSLYGAIEGLSELGHEVIKVFIIPRLKFISERVCNMQATDISNTERNAAGHIRALLAK
VCAPVLKTMRPSPDIIEDYKRDFGFLGPALHQSVMKARQTPSTTPTASTASSISVPSVTP
RITSTPIQRQISQSQPSQKFFVTKAANSPSTSSGNIVKIQQNNPQKIFIQAPKTVFVAAN
TQEHELEIDDLSHLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g10984.t3 | CDD | cd08050 | TAF6C | 205 | 420 | 2.34552E-97 |
| 9 | g10984.t3 | Gene3D | G3DSA:1.10.20.10 | Histone | 14 | 82 | 2.9E-25 |
| 10 | g10984.t3 | Gene3D | G3DSA:1.25.40.770 | - | 204 | 411 | 1.8E-66 |
| 8 | g10984.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 460 | 479 | - |
| 3 | g10984.t3 | PANTHER | PTHR10221:SF12 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 | 13 | 514 | 7.5E-213 |
| 4 | g10984.t3 | PANTHER | PTHR10221 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 | 13 | 514 | 7.5E-213 |
| 2 | g10984.t3 | Pfam | PF02969 | TATA box binding protein associated factor (TAF) | 19 | 81 | 4.3E-26 |
| 1 | g10984.t3 | Pfam | PF07571 | TAF6 C-terminal HEAT repeat domain | 300 | 389 | 3.9E-30 |
| 7 | g10984.t3 | SMART | SM00803 | TAF_cls | 17 | 81 | 2.4E-31 |
| 6 | g10984.t3 | SUPERFAMILY | SSF47113 | Histone-fold | 17 | 81 | 2.71E-14 |
| 5 | g10984.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 242 | 399 | 1.62E-5 |
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:0000124 | SAGA complex | CC |
| GO:0016251 | RNA polymerase II general transcription initiation factor activity | MF |
| GO:0046982 | protein heterodimerization activity | MF |
| GO:0046695 | SLIK (SAGA-like) complex | CC |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
| GO:0005669 | transcription factor TFIID complex | CC |
| GO:0006352 | DNA-templated transcription, initiation | BP |
KEGG
Orthology
- This transcript has been annotated with K03131 (transcription initiation factor TFIID subunit 6)
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.
