Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Transcription initiation factor TFIID subunit 11.

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_2 g7143 g7143.t1 isoform g7143.t1 21480376 21482277
chr_2 g7143 g7143.t1 exon g7143.t1.exon1 21480376 21480487
chr_2 g7143 g7143.t1 cds g7143.t1.CDS1 21480376 21480487
chr_2 g7143 g7143.t1 exon g7143.t1.exon2 21480547 21480810
chr_2 g7143 g7143.t1 cds g7143.t1.CDS2 21480547 21480810
chr_2 g7143 g7143.t1 exon g7143.t1.exon3 21480871 21481029
chr_2 g7143 g7143.t1 cds g7143.t1.CDS3 21480871 21481029
chr_2 g7143 g7143.t1 TSS g7143.t1 21481356 21481356
chr_2 g7143 g7143.t1 exon g7143.t1.exon4 21481603 21481608
chr_2 g7143 g7143.t1 cds g7143.t1.CDS4 21481603 21481608
chr_2 g7143 g7143.t1 exon g7143.t1.exon5 21481671 21481804
chr_2 g7143 g7143.t1 cds g7143.t1.CDS5 21481671 21481804
chr_2 g7143 g7143.t1 exon g7143.t1.exon6 21482036 21482132
chr_2 g7143 g7143.t1 cds g7143.t1.CDS6 21482036 21482132
chr_2 g7143 g7143.t1 exon g7143.t1.exon7 21482198 21482277
chr_2 g7143 g7143.t1 cds g7143.t1.CDS7 21482198 21482277
chr_2 g7143 g7143.t1 TTS g7143.t1 21482441 21482441

Sequences

>g7143.t1 Gene=g7143 Length=852
ATGGACTCAATTGACAAATTAGACCTTTTCCAATCACTAAAAGATGAATCATCTGACGAA
AAATATAAAATGCCAAATATCAAAAGTGAAGACGAGTCTGACAATAATGAAAACAATAAT
GATAACCAACACAATTCTGAAACTGAATATGAAGATTTAAGTTCTGCAATACCGAGTACT
TCTACAAACATATTTGATAAAGCATTCAAAAAGAAGCTTGATAAACAAAATAGAAAAGAA
GTTGAGGAAGAAGAACGTGAAAAGATGCTTGCTCTAGTATCTAACTTTACAGAAGCACAG
CTAGATCGATATGAAATGTATAGAAGGGCAGCATTTCCTAAAGCTCCAGTAAAAAGACTA
ATGCAAACAATTACAGGATGCTCTGTCTCACAAAATGTTGTAATAGCTATGAGTGGTATC
GCAAAAGTATTTGTCGGAGAAGTTGTTGAAGAAGCATTAGATGTTGCAGAAAGCTGGAAT
GATACAGGACCACTTCAACCCAAGCATTTACGAGAAGCTGTACGACGATTAAAAATTTAT
GTTGTAAATGGATGCGATGTGCTAACAGAAACACACCATGGTTGTAAAATTGAAAATTCA
CAATGTGTATGTGCTTATGGATGCAAAAGTGAATTTCGCTACACTACGAAGAAAGAATGC
ACCGACTCATTAAAGGGGAGATCATCTGATATATGTTCTCGTATCCCTTGCCTAAACGGT
GGAACCTGTATTCAAGTATCATTGAACCCTGGTTATAAATGCAAATGCGAAGGTACTCGG
TACTACGGAAATCGATGCCAAAGACCATGCCCTAAAGATGGCAACATACCTTATGAGTGC
GTAGAAATTTAG

>g7143.t1 Gene=g7143 Length=283
MDSIDKLDLFQSLKDESSDEKYKMPNIKSEDESDNNENNNDNQHNSETEYEDLSSAIPST
STNIFDKAFKKKLDKQNRKEVEEEEREKMLALVSNFTEAQLDRYEMYRRAAFPKAPVKRL
MQTITGCSVSQNVVIAMSGIAKVFVGEVVEEALDVAESWNDTGPLQPKHLREAVRRLKIY
VVNGCDVLTETHHGCKIENSQCVCAYGCKSEFRYTTKKECTDSLKGRSSDICSRIPCLNG
GTCIQVSLNPGYKCKCEGTRYYGNRCQRPCPKDGNIPYECVEI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g7143.t1 CDD cd08048 TAF11 96 178 9.50627E-52
7 g7143.t1 Gene3D G3DSA:1.10.20.10 Histone 96 181 2.6E-37
6 g7143.t1 Gene3D G3DSA:2.10.25.10 Laminin 228 268 4.2E-8
10 g7143.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 48 -
11 g7143.t1 MobiDBLite mobidb-lite consensus disorder prediction 1 58 -
3 g7143.t1 PANTHER PTHR13218 TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 11-RELATED 12 179 1.6E-51
2 g7143.t1 Pfam PF04719 hTAFII28-like protein conserved region 92 176 6.1E-38
1 g7143.t1 Pfam PF00008 EGF-like domain 232 265 2.0E-5
12 g7143.t1 ProSiteProfiles PS50026 EGF-like domain profile. 228 267 17.636
9 g7143.t1 SMART SM00181 egf_5 231 267 8.6E-4
4 g7143.t1 SUPERFAMILY SSF47113 Histone-fold 96 178 9.39E-35
5 g7143.t1 SUPERFAMILY SSF57196 EGF/Laminin 229 268 1.32E-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:0005634 nucleus CC
GO:0046982 protein heterodimerization activity MF
GO:0006367 transcription initiation from RNA polymerase II promoter 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.

Raw TPM values