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.t5 isoform g10984.t5 13162876 13163801
chr_1 g10984 g10984.t5 exon g10984.t5.exon1 13162876 13163639
chr_1 g10984 g10984.t5 cds g10984.t5.CDS1 13162876 13163639
chr_1 g10984 g10984.t5 exon g10984.t5.exon2 13163702 13163801
chr_1 g10984 g10984.t5 cds g10984.t5.CDS2 13163702 13163801
chr_1 g10984 g10984.t5 TSS g10984.t5 13163961 13163961
chr_1 g10984 g10984.t5 TTS g10984.t5 NA NA

Sequences

>g10984.t5 Gene=g10984 Length=864
ATGGAAGACAAAATAAAGAATCCTGAAATAAATTCTCAGCATTTCGGCACAAACTTATCG
CTTGAATCAATAAAAATTATTGCAGAATCAATTGGAATTGGAAATTTATCAGATTCTGCT
GCAAAAGAACTAAGTGATGATATTAGTTACAAATTAAAACAAATAGTGCAGGATGCTCAA
AAATTTATGAATCATGCAAAAAGAACACGCTTATCAATTGCTGATGTTGATCATTCATTG
AAAATAAGAAATATTGAACCGCAGTATGGATTCATATGTAAAGAATTTATACCGTTTCGA
TTTGCTAGCGGTGGCGGTCGAGAACTTTACTTCCAAGAAGAGAAAGAAGTAGATTTGAAT
GATGTTATGACTTCAACAGCCCCAAAAGCACCTCTTGAAGTGACATTAAGAGCACATTGG
CTTTGTGTTGATGGAATACAACCGACTATTCCAGAGAATCCTCCTCCTCTTTCAAAAGAC
GCTCAAATTCAAGATTCTGTAAATCCAATAAAGAAGATCGAGAAAGCTGATTTGAAAGAT
ACAAGTGGAAAACCTGCCATTAAAGCACACAAGCTTAAAACTCATGAAACTGTGCATATC
AAACAACTTGCACAGCATGAACTTTCAGTGGAACAACAATTTTATTACAAAGAAATCACA
GAAGCTTGTGTAGGTGCGGATGAGGCTCGTCGTGCTGAAGCTCTTCAATCGCTTTGTTGT
GATCCTGGAATACATGAAATGTTACCTAGAATGTGTACATTCATTGCAGAAGGTGTCAAA
ATAAATGTAGTACAAAACAATCTAGCAATTTTGATTTACCTTATGCGTATGGTTCGAGCA
CTTTTGGACAATCCTGCACTTTTT

>g10984.t5 Gene=g10984 Length=288
MEDKIKNPEINSQHFGTNLSLESIKIIAESIGIGNLSDSAAKELSDDISYKLKQIVQDAQ
KFMNHAKRTRLSIADVDHSLKIRNIEPQYGFICKEFIPFRFASGGGRELYFQEEKEVDLN
DVMTSTAPKAPLEVTLRAHWLCVDGIQPTIPENPPPLSKDAQIQDSVNPIKKIEKADLKD
TSGKPAIKAHKLKTHETVHIKQLAQHELSVEQQFYYKEITEACVGADEARRAEALQSLCC
DPGIHEMLPRMCTFIAEGVKINVVQNNLAILIYLMRMVRALLDNPALF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10984.t5 CDD cd08050 TAF6C 205 288 0
6 g10984.t5 Gene3D G3DSA:1.10.20.10 Histone 14 82 0
7 g10984.t5 Gene3D G3DSA:1.25.40.770 - 204 288 0
2 g10984.t5 PANTHER PTHR10221:SF12 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 13 287 0
3 g10984.t5 PANTHER PTHR10221 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 6 13 287 0
1 g10984.t5 Pfam PF02969 TATA box binding protein associated factor (TAF) 19 81 0
5 g10984.t5 SMART SM00803 TAF_cls 17 81 0
4 g10984.t5 SUPERFAMILY SSF47113 Histone-fold 17 81 0

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 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. There were no conditions that were differentially expressed