Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription initiation factor TFIID subunit 6.

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_1 g10984 g10984.t4 TTS g10984.t4 13161806 13161806
chr_1 g10984 g10984.t4 isoform g10984.t4 13162686 13163801
chr_1 g10984 g10984.t4 exon g10984.t4.exon1 13162686 13162802
chr_1 g10984 g10984.t4 cds g10984.t4.CDS1 13162686 13162802
chr_1 g10984 g10984.t4 exon g10984.t4.exon2 13162864 13163639
chr_1 g10984 g10984.t4 cds g10984.t4.CDS2 13162864 13163639
chr_1 g10984 g10984.t4 exon g10984.t4.exon3 13163702 13163801
chr_1 g10984 g10984.t4 cds g10984.t4.CDS3 13163702 13163801
chr_1 g10984 g10984.t4 TSS g10984.t4 13163961 13163961

Sequences

>g10984.t4 Gene=g10984 Length=993
ATGGAAGACAAAATAAAGAATCCTGAAATAAATTCTCAGCATTTCGGCACAAACTTATCG
CTTGAATCAATAAAAATTATTGCAGAATCAATTGGAATTGGAAATTTATCAGATTCTGCT
GCAAAAGAACTAAGTGATGATATTAGTTACAAATTAAAACAAATAGTGCAGGATGCTCAA
AAATTTATGAATCATGCAAAAAGAACACGCTTATCAATTGCTGATGTTGATCATTCATTG
AAAATAAGAAATATTGAACCGCAGTATGGATTCATATGTAAAGAATTTATACCGTTTCGA
TTTGCTAGCGGTGGCGGTCGAGAACTTTACTTCCAAGAAGAGAAAGAAGTAGATTTGAAT
GATGTTATGACTTCAACAGCCCCAAAAGCACCTCTTGAAGTGACATTAAGAGCACATTGG
CTTTGTGTTGATGGAATACAACCGACTATTCCAGAGAATCCTCCTCCTCTTTCAAAAGAC
GCTCAAATTCAAGATTCTGTAAATCCAATAAAGAAGATCGAGAAAGCTGATTTGAAAGAT
ACAAGTGGAAAACCTGCCATTAAAGCACACAAGCTTAAAACTCATGAAACTGTGCATATC
AAACAACTTGCACAGCATGAACTTTCAGTGGAACAACAATTTTATTACAAAGAAATCACA
GAAGCTTGTGTAGGTGCGGATGAGGCTCGTCGTGCTGAAGCTCTTCAATCGCTTTGTTGT
GATCCTGGAATACATGAAATGTTACCTAGAATGTGTACATTCATTGCAGAAGGTGTCAAA
ATAAATGTAGTACAAAACAATCTAGCAATTTTGATTTACCTTATGCGTATGGTTCGAGCA
CTTTTGGACAATCCTGCACTTTTTCTTGAAAAATATCTTCATGAATTAATTCCATCAGTT
TCAACTTGCATTGTGTCAAAGCAATTGTGCCAACGTCCAGAAGTTGATAATCATTGGGCT
CTGAGAGATTTTGCTGCAAAATTAATGGCGCAA

>g10984.t4 Gene=g10984 Length=331
MEDKIKNPEINSQHFGTNLSLESIKIIAESIGIGNLSDSAAKELSDDISYKLKQIVQDAQ
KFMNHAKRTRLSIADVDHSLKIRNIEPQYGFICKEFIPFRFASGGGRELYFQEEKEVDLN
DVMTSTAPKAPLEVTLRAHWLCVDGIQPTIPENPPPLSKDAQIQDSVNPIKKIEKADLKD
TSGKPAIKAHKLKTHETVHIKQLAQHELSVEQQFYYKEITEACVGADEARRAEALQSLCC
DPGIHEMLPRMCTFIAEGVKINVVQNNLAILIYLMRMVRALLDNPALFLEKYLHELIPSV
STCIVSKQLCQRPEVDNHWALRDFAAKLMAQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g10984.t4 CDD cd08050 TAF6C 205 331 6.15132E-65
9 g10984.t4 Coils Coil Coil 325 331 -
7 g10984.t4 Gene3D G3DSA:1.10.20.10 Histone 14 82 1.3E-25
8 g10984.t4 Gene3D G3DSA:1.25.40.770 - 204 331 1.8E-42
3 g10984.t4 PANTHER PTHR10221:SF12 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 13 331 1.3E-155
4 g10984.t4 PANTHER PTHR10221 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 13 331 1.3E-155
2 g10984.t4 Pfam PF02969 TATA box binding protein associated factor (TAF) 19 81 2.0E-26
1 g10984.t4 Pfam PF07571 TAF6 C-terminal HEAT repeat domain 300 331 1.8E-7
6 g10984.t4 SMART SM00803 TAF_cls 17 81 2.4E-31
5 g10984.t4 SUPERFAMILY SSF47113 Histone-fold 17 81 1.04E-14

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

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. There were no conditions that were differentially expressed