Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription factor Dp.

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_4 g16140 g16140.t1 TTS g16140.t1 8349740 8349740
chr_4 g16140 g16140.t1 isoform g16140.t1 8349940 8352367
chr_4 g16140 g16140.t1 exon g16140.t1.exon1 8349940 8350088
chr_4 g16140 g16140.t1 cds g16140.t1.CDS1 8349940 8350088
chr_4 g16140 g16140.t1 exon g16140.t1.exon2 8350149 8350232
chr_4 g16140 g16140.t1 cds g16140.t1.CDS2 8350149 8350232
chr_4 g16140 g16140.t1 exon g16140.t1.exon3 8350291 8350373
chr_4 g16140 g16140.t1 cds g16140.t1.CDS3 8350291 8350373
chr_4 g16140 g16140.t1 exon g16140.t1.exon4 8350434 8351018
chr_4 g16140 g16140.t1 cds g16140.t1.CDS4 8350434 8351018
chr_4 g16140 g16140.t1 exon g16140.t1.exon5 8351679 8351743
chr_4 g16140 g16140.t1 cds g16140.t1.CDS5 8351679 8351743
chr_4 g16140 g16140.t1 exon g16140.t1.exon6 8351892 8351948
chr_4 g16140 g16140.t1 cds g16140.t1.CDS6 8351892 8351948
chr_4 g16140 g16140.t1 exon g16140.t1.exon7 8352157 8352218
chr_4 g16140 g16140.t1 cds g16140.t1.CDS7 8352157 8352218
chr_4 g16140 g16140.t1 exon g16140.t1.exon8 8352325 8352367
chr_4 g16140 g16140.t1 cds g16140.t1.CDS8 8352325 8352367
chr_4 g16140 g16140.t1 TSS g16140.t1 8352443 8352443

Sequences

>g16140.t1 Gene=g16140 Length=1128
ATGAATTCTCAAAGCACATATTTTCTTGTGTCTGATGAAAATGGTACAAAAAAATTGATT
GCAACATCATCGACTGGTATAAAAAAGGAACATGTCATGTCACAATCAATTATGAACATT
GTTCCAAAACAAACATTTCAACGAAATAACAGCAATCAAACAAAACAACTAAGTACCTCA
GTTATCGTTCAAAGAGCAACCACAGAAAAACCATATGCACGTAAAAGCCTCCCAGCAACA
ACTTCCTCATCACATTTTTCCCCATCATTTAAAAAGACAGACAAAAAGAGAAATGACAAG
CCAGGCAAAGGTTTAAGGCATTTTTCAATGCGTGTCTGTCAGAAAGTAAAAGAGAAGGGA
ATCACATCATACAATGAAGTTGCAGATGAGTTGGTACTTGAAGAAAGTGAAGATAACTGT
GGAGGAACATCATCAGCTGCAAATGGACAATCCTATGATCAAAAAAATATTCGTCGACGT
GTCTATGATGCTCTCAATGTTTTAATGGCAATGAACATTATCTCGAAAGAAAAGAAAGAA
ATAAAATGGCTTGGATTGCCAACATCATCAGTACAAGAATGTGAAGAGATTGAAATTGAA
AACCAACAGACAAGAAAAAGAATTGAAGAGAAACAGCAGCAATTGCGTGAACTTGTATTA
AAACATGTCTCATTCAGAAATTTAATTGAAAGAAATAAGAATTTAGAAAAACAAGGCATC
GTGCCTTCTGTCAGCTCTGCTGTACATTTGCCATTTATTGTCATCAACACAAATAAAAAG
ACACACATAAATTGCAATATTTCAAATGACAAACGAGAATATTTATTAAAATTTGATGAC
AAATTTGAAGTGCAAGATGATTTTGAAGTATTAAAACGAATGGGAATGCTTTTGGGTATG
GATAAAGGTGAATCATCGTCAAGTGACATTGAAAAATTAAAGAAACTGGCTCCAAAAGCT
TATCACAAATACATTGAAATGTATGGAAATGGATACCTTGCATCTGAAAATCAGGACGAG
AATATTATTGAAGAAGATTGGACAATGGATCAAACACAAAGTAGCACTTACACACATGAC
TCAACATTTGATCAAGAATATATCGAAGAGGAAATTGCAAATGATTAA

>g16140.t1 Gene=g16140 Length=375
MNSQSTYFLVSDENGTKKLIATSSTGIKKEHVMSQSIMNIVPKQTFQRNNSNQTKQLSTS
VIVQRATTEKPYARKSLPATTSSSHFSPSFKKTDKKRNDKPGKGLRHFSMRVCQKVKEKG
ITSYNEVADELVLEESEDNCGGTSSAANGQSYDQKNIRRRVYDALNVLMAMNIISKEKKE
IKWLGLPTSSVQECEEIEIENQQTRKRIEEKQQQLRELVLKHVSFRNLIERNKNLEKQGI
VPSVSSAVHLPFIVINTNKKTHINCNISNDKREYLLKFDDKFEVQDDFEVLKRMGMLLGM
DKGESSSSDIEKLKKLAPKAYHKYIEMYGNGYLASENQDENIIEEDWTMDQTQSSTYTHD
STFDQEYIEEEIAND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16140.t1 CDD cd14458 DP_DD 190 294 6.27513E-42
9 g16140.t1 Coils Coil Coil 194 221 -
8 g16140.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 94 190 5.8E-40
7 g16140.t1 Gene3D G3DSA:1.20.140.80 - 191 332 2.5E-50
16 g16140.t1 MobiDBLite mobidb-lite consensus disorder prediction 69 105 -
15 g16140.t1 MobiDBLite mobidb-lite consensus disorder prediction 74 88 -
14 g16140.t1 MobiDBLite mobidb-lite consensus disorder prediction 89 105 -
3 g16140.t1 PANTHER PTHR12548:SF5 TRANSCRIPTION FACTOR DP-2 65 373 3.8E-101
4 g16140.t1 PANTHER PTHR12548 TRANSCRIPTION FACTOR DP 65 373 3.8E-101
10 g16140.t1 PIRSF PIRSF009404 Txn_factor_DP 2 371 1.4E-104
2 g16140.t1 Pfam PF02319 E2F/DP family winged-helix DNA-binding domain 103 185 5.4E-22
1 g16140.t1 Pfam PF08781 Transcription factor DP 192 327 1.8E-50
12 g16140.t1 SMART SM01372 E2F_TDP_2 100 185 1.0E-30
13 g16140.t1 SMART SM01138 DP_2 192 335 6.4E-61
5 g16140.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 103 186 3.67E-21
6 g16140.t1 SUPERFAMILY SSF144074 E2F-DP heterodimerization region 191 332 2.22E-45

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:0005667 transcription regulator complex CC
GO:0051726 regulation of cell cycle 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