Gene loci information

Transcript annotation

  • This transcript has been annotated as Heat shock factor.

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_3 g3611 g3611.t1 TTS g3611.t1 26742736 26742736
chr_3 g3611 g3611.t1 isoform g3611.t1 26743487 26747182
chr_3 g3611 g3611.t1 exon g3611.t1.exon1 26743487 26743496
chr_3 g3611 g3611.t1 cds g3611.t1.CDS1 26743487 26743496
chr_3 g3611 g3611.t1 exon g3611.t1.exon2 26743556 26743572
chr_3 g3611 g3611.t1 cds g3611.t1.CDS2 26743556 26743572
chr_3 g3611 g3611.t1 exon g3611.t1.exon3 26743632 26743660
chr_3 g3611 g3611.t1 cds g3611.t1.CDS3 26743632 26743660
chr_3 g3611 g3611.t1 exon g3611.t1.exon4 26743725 26743800
chr_3 g3611 g3611.t1 cds g3611.t1.CDS4 26743725 26743800
chr_3 g3611 g3611.t1 exon g3611.t1.exon5 26744013 26744054
chr_3 g3611 g3611.t1 cds g3611.t1.CDS5 26744013 26744054
chr_3 g3611 g3611.t1 exon g3611.t1.exon6 26744248 26744304
chr_3 g3611 g3611.t1 cds g3611.t1.CDS6 26744248 26744304
chr_3 g3611 g3611.t1 exon g3611.t1.exon7 26744553 26744798
chr_3 g3611 g3611.t1 cds g3611.t1.CDS7 26744553 26744798
chr_3 g3611 g3611.t1 exon g3611.t1.exon8 26744860 26745948
chr_3 g3611 g3611.t1 cds g3611.t1.CDS8 26744860 26745948
chr_3 g3611 g3611.t1 exon g3611.t1.exon9 26747078 26747182
chr_3 g3611 g3611.t1 cds g3611.t1.CDS9 26747078 26747182
chr_3 g3611 g3611.t1 TSS g3611.t1 26747196 26747196

Sequences

>g3611.t1 Gene=g3611 Length=1671
ATGCATCCGATCGAGAGTGGAAATTTAGGTGTCCCTGCATTCTTGGCAAAATTATGGCGA
TTAGTTGAAGATTCTGATACAAACGAACTAATTTCTTGGAGTCAAGATGGCAAAAGTTTT
TTCATACAAAATCAAGCAAAATTTGCAAAAGAATTACTTCCTCTTAATTACAAGCACAAC
AATATGGCTAGTTTTATTCGACAGCTTAATATGTATGGCTTTCATAAAATAACTTCAATC
GACAATGGCGGTTTGAAATTTGATAAAGATGAAATGGAATTTTCTCATCCTTATTTTCAA
AAAGGTCATCCATATTTACTTGAGCATATTAAACGAAAGATTGCACATCCAAAACAACCG
GAAGCTGATAAAACAACTGTAACAAAAGTGGAGACTATGAATCGAGTTTTACATGAAGTC
AAAAATATGAGGGGTCGTCAAGACTCCTTGGATACTCGTTTCAGTGCTATGAAACAGGAG
AATGAAGCATTATGGCGTGAAGTCGCAATTTTACGACAAAAACATATGAAGCAACAACAA
ATTGTAAACAAATTAATACAATTTTTGGTAACAATTGTTCAACCAAATCGAGGTGGTCTT
GGAAGCGGTATTGGCAAACGTCGTTATCAGTTAATGATCAATGATGCACCACAAGCAAAA
GTTAAAAAAACAAATAATGGTCCAATTATAAGCGAACTTACTGAAGAATTGCTAGATGAT
GTTGAATCTGATCTAGATAACGATTCATGTAATTTTACAAACGTACAATCACCTGAATCA
GACACATGCAAAAATGAAGATAAAGAAACAACTTCTTTTGACAAATGTTTGGAAAGATGT
TTAGAAATTGACGATAATGTTGATGAAATTGATACAAACAATATGAAAGAATATTGCAAA
ACAATATTTAAAAAGAAACAAAATATTAATGACAAAGCAACAAGCTCAAAAATGGACAAG
CAACAAATAAAGAAAGAAGCTACTGAGAATGCTTCTATTGTTCAAAAATCTACGGGAAAA
AGTTTGCTCATACCATCAAAAGATAATAAAACTACAACAGATATTACATATAATATTATT
AACGCTGATAATGAGATGACCATAACAAATAATTCAGCTGGTATAACTAATACAAAACCA
AAAGAAGATGGATTAACTGAAACACAATATCAAAATTTCGATGATACCTCACAAAACACA
GATCTTCTAGATGATGAGGATTTATTTAAGTTTGTTGATAAAAAAGAGCAGCAACAGACT
TCTGGAGATGATTCGCTTCTAATAACAAAATATAATCGATCAAATTCAACAGACATCATG
GGGTTAAATTCACTAGAAGATTACTCTAATCATATAGACACCGTTCAATCTGATTTAGAT
TCGTTGAAAGATTTATTGCATAACGATGCTTATCAGTTGGATACAAATCAATTATTAGGG
AATGGTGCTGTTTACACTATGCCTTTTGGGAACTATGATGCTGATACTATTTCAAAGATG
GCTGAAGCTGATGCAACCTTGCTGAAGATACAAGATGATCTCTTTGGTAATGACGATTTG
ATTGGTTATGAAATGTCGCCAGCTAACATGGAACTTTTTGCTGAAGATAAAAAAGACGAC
CAAACATCACCAGGATCTGAAGTTCAACAATGCATAAAAAGGATTACATGA

>g3611.t1 Gene=g3611 Length=556
MHPIESGNLGVPAFLAKLWRLVEDSDTNELISWSQDGKSFFIQNQAKFAKELLPLNYKHN
NMASFIRQLNMYGFHKITSIDNGGLKFDKDEMEFSHPYFQKGHPYLLEHIKRKIAHPKQP
EADKTTVTKVETMNRVLHEVKNMRGRQDSLDTRFSAMKQENEALWREVAILRQKHMKQQQ
IVNKLIQFLVTIVQPNRGGLGSGIGKRRYQLMINDAPQAKVKKTNNGPIISELTEELLDD
VESDLDNDSCNFTNVQSPESDTCKNEDKETTSFDKCLERCLEIDDNVDEIDTNNMKEYCK
TIFKKKQNINDKATSSKMDKQQIKKEATENASIVQKSTGKSLLIPSKDNKTTTDITYNII
NADNEMTITNNSAGITNTKPKEDGLTETQYQNFDDTSQNTDLLDDEDLFKFVDKKEQQQT
SGDDSLLITKYNRSNSTDIMGLNSLEDYSNHIDTVQSDLDSLKDLLHNDAYQLDTNQLLG
NGAVYTMPFGNYDADTISKMAEADATLLKIQDDLFGNDDLIGYEMSPANMELFAEDKKDD
QTSPGSEVQQCIKRIT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3611.t1 Coils Coil Coil 445 465 -
8 g3611.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 9 113 4.6E-43
2 g3611.t1 PANTHER PTHR10015 HEAT SHOCK TRANSCRIPTION FACTOR 6 219 2.6E-77
3 g3611.t1 PANTHER PTHR10015:SF274 HEAT SHOCK FACTOR PROTEIN 1 6 219 2.6E-77
4 g3611.t1 PRINTS PR00056 Heat shock factor (HSF) domain signature 14 37 3.8E-17
6 g3611.t1 PRINTS PR00056 Heat shock factor (HSF) domain signature 52 64 3.8E-17
5 g3611.t1 PRINTS PR00056 Heat shock factor (HSF) domain signature 65 77 3.8E-17
1 g3611.t1 Pfam PF00447 HSF-type DNA-binding 14 113 8.4E-32
10 g3611.t1 ProSitePatterns PS00434 HSF-type DNA-binding domain signature. 53 77 -
11 g3611.t1 SMART SM00415 hsfneu3 10 113 4.0E-59
7 g3611.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 10 113 7.21E-40

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:0006355 regulation of transcription, DNA-templated BP
GO:0043565 sequence-specific DNA binding MF
GO:0003700 DNA-binding transcription factor activity MF

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