General information for g4040.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeotic protein ultrabithorax.
Parent gene
- The parent gene g4040 is located on chr_3: 29932469..29993697 (- 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_3 | g4040 | g4040.t1 | isoform | g4040.t1 | 29932469 | 29993697 |
| chr_3 | g4040 | g4040.t1 | exon | g4040.t1.exon1 | 29932469 | 29932598 |
| chr_3 | g4040 | g4040.t1 | cds | g4040.t1.CDS1 | 29932469 | 29932598 |
| chr_3 | g4040 | g4040.t1 | exon | g4040.t1.exon2 | 29932665 | 29932821 |
| chr_3 | g4040 | g4040.t1 | cds | g4040.t1.CDS2 | 29932665 | 29932821 |
| chr_3 | g4040 | g4040.t1 | exon | g4040.t1.exon3 | 29976868 | 29976918 |
| chr_3 | g4040 | g4040.t1 | cds | g4040.t1.CDS3 | 29976868 | 29976918 |
| chr_3 | g4040 | g4040.t1 | exon | g4040.t1.exon4 | 29993445 | 29993697 |
| chr_3 | g4040 | g4040.t1 | cds | g4040.t1.CDS4 | 29993445 | 29993697 |
| chr_3 | g4040 | g4040.t1 | TSS | g4040.t1 | NA | NA |
| chr_3 | g4040 | g4040.t1 | TTS | g4040.t1 | NA | NA |
Sequences
>g4040.t1 Gene=g4040 Length=591
ATGTCTGGAATTCTAACCGGCAATAATGGCTCACAAAATTCAGCACCTGTTCGTCCATCA
CCTGCACACCCGATTCACGAGTTGGTGGTTATATCGATGCATCAGGTGGATCACCAGTCA
GTCGTACTGGTTCATCTGCAACCGGTGGCGCATGGAACTCAAATTGCACCATCGGCAACA
ACCGGCTCGCAATCATCGGCTTCAGCAAGTTTACATCAGAATCATACTTTTTATCCATGG
ATGGCTATTGCAGGTAAGAGATATTCAGAATCTCTTGCGGGGACGCTGTTGCCAGACTGG
ATAGGTGCAAATGGATTAAGGAGAAGAGGCCGCCAAACATACACACGATACCAAACGCTC
GAACTTGAAAAAGAGTTCCACACAAACCACTATCTCACTCGACGACGCCGAATAGAGATG
GCTCATGCACTTTGTCTTACCGAGCGACAAATTAAAATTTGGTTTCAAAATCGACGAATG
AAATTAAAAAAGGAAATACAGGCCATCAAAGAATTGAATGAGCAGGAGAAGCAAGCACAA
GCACAAAAGGCAGCATTAGTTGCGCAAGGTCATACAATAGAGGGAACTTAG
>g4040.t1 Gene=g4040 Length=196
MSGILTGNNGSQNSAPVRPSPAHPIHELVVISMHQVDHQSVVLVHLQPVAHGTQIAPSAT
TGSQSSASASLHQNHTFYPWMAIAGKRYSESLAGTLLPDWIGANGLRRRGRQTYTRYQTL
ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQ
AQKAALVAQGHTIEGT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4040.t1 | CDD | cd00086 | homeodomain | 108 | 165 | 2.28668E-23 |
| 11 | g4040.t1 | Coils | Coil | Coil | 159 | 189 | - |
| 10 | g4040.t1 | Gene3D | G3DSA:1.10.10.60 | - | 71 | 168 | 6.0E-34 |
| 15 | g4040.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 20 | - |
| 16 | g4040.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 18 | - |
| 2 | g4040.t1 | PANTHER | PTHR45659:SF15 | HOMEOTIC PROTEIN ULTRABITHORAX | 45 | 193 | 2.3E-75 |
| 3 | g4040.t1 | PANTHER | PTHR45659 | HOMEOBOX PROTEIN HOX | 45 | 193 | 2.3E-75 |
| 7 | g4040.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 76 | 83 | 8.8E-5 |
| 8 | g4040.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 108 | 123 | 8.8E-5 |
| 5 | g4040.t1 | PRINTS | PR00024 | Homeobox signature | 129 | 140 | 3.3E-8 |
| 4 | g4040.t1 | PRINTS | PR00024 | Homeobox signature | 144 | 154 | 3.3E-8 |
| 6 | g4040.t1 | PRINTS | PR00024 | Homeobox signature | 154 | 163 | 3.3E-8 |
| 1 | g4040.t1 | Pfam | PF00046 | Homeodomain | 108 | 164 | 1.2E-20 |
| 14 | g4040.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 140 | 163 | - |
| 17 | g4040.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 105 | 165 | 20.811 |
| 13 | g4040.t1 | SMART | SM00389 | HOX_1 | 107 | 169 | 4.5E-24 |
| 9 | g4040.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 94 | 164 | 1.03E-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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0003700 | DNA-binding transcription factor activity | MF |
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. There were no conditions that were differentially expressed