General information for g16140.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transcription factor Dp.
Parent gene
- The parent gene g16140 is located on chr_4: 8352367..8355397 (- strand)
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.t3 | TTS | g16140.t3 | 8349740 | 8349740 |
| chr_4 | g16140 | g16140.t3 | isoform | g16140.t3 | 8349940 | 8352367 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon1 | 8349940 | 8350088 |
| chr_4 | g16140 | g16140.t3 | cds | g16140.t3.CDS1 | 8349940 | 8350088 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon2 | 8350149 | 8350232 |
| chr_4 | g16140 | g16140.t3 | cds | g16140.t3.CDS2 | 8350149 | 8350232 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon3 | 8350291 | 8350373 |
| chr_4 | g16140 | g16140.t3 | cds | g16140.t3.CDS3 | 8350291 | 8350373 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon4 | 8350434 | 8351010 |
| chr_4 | g16140 | g16140.t3 | cds | g16140.t3.CDS4 | 8350434 | 8351010 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon5 | 8351679 | 8351743 |
| chr_4 | g16140 | g16140.t3 | cds | g16140.t3.CDS5 | 8351679 | 8351691 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon6 | 8352157 | 8352218 |
| chr_4 | g16140 | g16140.t3 | exon | g16140.t3.exon7 | 8352325 | 8352367 |
| chr_4 | g16140 | g16140.t3 | TSS | g16140.t3 | 8352443 | 8352443 |
Sequences
>g16140.t3 Gene=g16140 Length=1063
ATGAATTCTCAAAGCACATATTTTCTTGTGTCTGATGAAAATGGTACAAAAAAATTGATT
GCAACATCATCGACTGGTATAAAAAAGGAACATGTCATGTCACAAAAACAACTAAGTACC
TCAGTTATCGTTCAAAGAGCAACCACAGAAAAACCATATGCACGTAAAAGCAACAACTTC
CTCATCACATTTTTCCCCATCATTTAAAAAGACAGACAAAAAGAGAAATGACAAGCCAGG
CAAAGGTTTAAGGCATTTTTCAATGCGTGTCTGTCAGAAAGTAAAAGAGAAGGGAATCAC
ATCATACAATGAAGTTGCAGATGAGTTGGTACTTGAAGAAAGTGAAGATAACTGTGGAGG
AACATCATCAGCTGCAAATGGACAATCCTATGATCAAAAAAATATTCGTCGACGTGTCTA
TGATGCTCTCAATGTTTTAATGGCAATGAACATTATCTCGAAAGAAAAGAAAGAAATAAA
ATGGCTTGGATTGCCAACATCATCAGTACAAGAATGTGAAGAGATTGAAATTGAAAACCA
ACAGACAAGAAAAAGAATTGAAGAGAAACAGCAGCAATTGCGTGAACTTGTATTAAAACA
TGTCTCATTCAGAAATTTAATTGAAAGAAATAAGAATTTAGAAAAACAAGGCATCGTGCC
TTCTGTCAGCTCTGCTGTACATTTGCCATTTATTGTCATCAACACAAATAAAAAGACACA
CATAAATTGCAATATTTCAAATGACAAACGAGAATATTTATTAAAATTTGATGACAAATT
TGAAGTGCAAGATGATTTTGAAGTATTAAAACGAATGGGAATGCTTTTGGGTATGGATAA
AGGTGAATCATCGTCAAGTGACATTGAAAAATTAAAGAAACTGGCTCCAAAAGCTTATCA
CAAATACATTGAAATGTATGGAAATGGATACCTTGCATCTGAAAATCAGGACGAGAATAT
TATTGAAGAAGATTGGACAATGGATCAAACACAAAGTAGCACTTACACACATGACTCAAC
ATTTGATCAAGAATATATCGAAGAGGAAATTGCAAATGATTAA
>g16140.t3 Gene=g16140 Length=301
MHVKATTSSSHFSPSFKKTDKKRNDKPGKGLRHFSMRVCQKVKEKGITSYNEVADELVLE
ESEDNCGGTSSAANGQSYDQKNIRRRVYDALNVLMAMNIISKEKKEIKWLGLPTSSVQEC
EEIEIENQQTRKRIEEKQQQLRELVLKHVSFRNLIERNKNLEKQGIVPSVSSAVHLPFIV
INTNKKTHINCNISNDKREYLLKFDDKFEVQDDFEVLKRMGMLLGMDKGESSSSDIEKLK
KLAPKAYHKYIEMYGNGYLASENQDENIIEEDWTMDQTQSSTYTHDSTFDQEYIEEEIAN
D
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16140.t3 | CDD | cd14458 | DP_DD | 116 | 220 | 3.47168E-42 |
| 9 | g16140.t3 | Coils | Coil | Coil | 120 | 147 | - |
| 8 | g16140.t3 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 20 | 116 | 3.8E-40 |
| 7 | g16140.t3 | Gene3D | G3DSA:1.20.140.80 | - | 117 | 258 | 1.5E-50 |
| 15 | g16140.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 32 | - |
| 14 | g16140.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 15 | 32 | - |
| 3 | g16140.t3 | PANTHER | PTHR12548:SF5 | TRANSCRIPTION FACTOR DP-2 | 12 | 299 | 4.1E-101 |
| 4 | g16140.t3 | PANTHER | PTHR12548 | TRANSCRIPTION FACTOR DP | 12 | 299 | 4.1E-101 |
| 10 | g16140.t3 | PIRSF | PIRSF009404 | Txn_factor_DP | 1 | 297 | 2.0E-103 |
| 2 | g16140.t3 | Pfam | PF02319 | E2F/DP family winged-helix DNA-binding domain | 29 | 111 | 3.6E-22 |
| 1 | g16140.t3 | Pfam | PF08781 | Transcription factor DP | 118 | 253 | 1.1E-50 |
| 12 | g16140.t3 | SMART | SM01372 | E2F_TDP_2 | 26 | 111 | 1.0E-30 |
| 13 | g16140.t3 | SMART | SM01138 | DP_2 | 118 | 261 | 6.4E-61 |
| 5 | g16140.t3 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 29 | 112 | 2.45E-21 |
| 6 | g16140.t3 | SUPERFAMILY | SSF144074 | E2F-DP heterodimerization region | 117 | 258 | 1.33E-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
- This transcript has been annotated with K04683 (transcription factor Dp-1)
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. There were no conditions that were differentially expressed