Gene loci information

Transcript annotation

  • This transcript has been annotated as Transcription factor Dp-1.

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.t4 TTS g16140.t4 8349740 8349740
chr_4 g16140 g16140.t4 isoform g16140.t4 8350434 8352367
chr_4 g16140 g16140.t4 exon g16140.t4.exon1 8350434 8351018
chr_4 g16140 g16140.t4 cds g16140.t4.CDS1 8350436 8351018
chr_4 g16140 g16140.t4 exon g16140.t4.exon2 8351679 8351743
chr_4 g16140 g16140.t4 cds g16140.t4.CDS2 8351679 8351743
chr_4 g16140 g16140.t4 exon g16140.t4.exon3 8351892 8351948
chr_4 g16140 g16140.t4 cds g16140.t4.CDS3 8351892 8351948
chr_4 g16140 g16140.t4 exon g16140.t4.exon4 8352157 8352218
chr_4 g16140 g16140.t4 cds g16140.t4.CDS4 8352157 8352218
chr_4 g16140 g16140.t4 exon g16140.t4.exon5 8352325 8352367
chr_4 g16140 g16140.t4 cds g16140.t4.CDS5 8352325 8352367
chr_4 g16140 g16140.t4 TSS g16140.t4 8352443 8352443

Sequences

>g16140.t4 Gene=g16140 Length=812
ATGAATTCTCAAAGCACATATTTTCTTGTGTCTGATGAAAATGGTACAAAAAAATTGATT
GCAACATCATCGACTGGTATAAAAAAGGAACATGTCATGTCACAATCAATTATGAACATT
GTTCCAAAACAAACATTTCAACGAAATAACAGCAATCAAACAAAACAACTAAGTACCTCA
GTTATCGTTCAAAGAGCAACCACAGAAAAACCATATGCACGTAAAAGCCTCCCAGCAACA
ACTTCCTCATCACATTTTTCCCCATCATTTAAAAAGACAGACAAAAAGAGAAATGACAAG
CCAGGCAAAGGTTTAAGGCATTTTTCAATGCGTGTCTGTCAGAAAGTAAAAGAGAAGGGA
ATCACATCATACAATGAAGTTGCAGATGAGTTGGTACTTGAAGAAAGTGAAGATAACTGT
GGAGGAACATCATCAGCTGCAAATGGACAATCCTATGATCAAAAAAATATTCGTCGACGT
GTCTATGATGCTCTCAATGTTTTAATGGCAATGAACATTATCTCGAAAGAAAAGAAAGAA
ATAAAATGGCTTGGATTGCCAACATCATCAGTACAAGAATGTGAAGAGATTGAAATTGAA
AACCAACAGACAAGAAAAAGAATTGAAGAGAAACAGCAGCAATTGCGTGAACTTGTATTA
AAACATGTCTCATTCAGAAATTTAATTGAAAGAAATAAGAATTTAGAAAAACAAGGCATC
GTGCCTTCTGTCAGCTCTGCTGTACATTTGCCATTTATTGTCATCAACACAAATAAAAAG
ACACACATAAATTGCAATATTTCAAATGACAA

>g16140.t4 Gene=g16140 Length=270
MNSQSTYFLVSDENGTKKLIATSSTGIKKEHVMSQSIMNIVPKQTFQRNNSNQTKQLSTS
VIVQRATTEKPYARKSLPATTSSSHFSPSFKKTDKKRNDKPGKGLRHFSMRVCQKVKEKG
ITSYNEVADELVLEESEDNCGGTSSAANGQSYDQKNIRRRVYDALNVLMAMNIISKEKKE
IKWLGLPTSSVQECEEIEIENQQTRKRIEEKQQQLRELVLKHVSFRNLIERNKNLEKQGI
VPSVSSAVHLPFIVINTNKKTHINCNISND

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g16140.t4 CDD cd14458 DP_DD 190 270 7.04613E-29
8 g16140.t4 Coils Coil Coil 194 221 -
7 g16140.t4 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 94 190 3.0E-40
6 g16140.t4 Gene3D G3DSA:1.20.140.80 - 191 270 1.0E-24
15 g16140.t4 MobiDBLite mobidb-lite consensus disorder prediction 69 105 -
14 g16140.t4 MobiDBLite mobidb-lite consensus disorder prediction 74 88 -
13 g16140.t4 MobiDBLite mobidb-lite consensus disorder prediction 89 105 -
3 g16140.t4 PANTHER PTHR12548 TRANSCRIPTION FACTOR DP 43 270 8.2E-80
9 g16140.t4 PIRSF PIRSF009404 Txn_factor_DP 2 270 1.5E-85
2 g16140.t4 Pfam PF02319 E2F/DP family winged-helix DNA-binding domain 103 185 3.0E-22
1 g16140.t4 Pfam PF08781 Transcription factor DP 192 270 3.0E-26
11 g16140.t4 SMART SM01372 E2F_TDP_2 100 185 1.0E-30
12 g16140.t4 SMART SM01138 DP_2 192 270 7.7E-15
4 g16140.t4 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 103 186 2.04E-21
5 g16140.t4 SUPERFAMILY SSF144074 E2F-DP heterodimerization region 191 270 7.85E-25

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

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.

Raw TPM values