General information for g414.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein vnd.
Parent gene
- The parent gene g414 is located on chr_3: 3278747..3279319 (- 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 | g414 | g414.t1 | isoform | g414.t1 | 3278747 | 3279319 |
| chr_3 | g414 | g414.t1 | exon | g414.t1.exon1 | 3278747 | 3279319 |
| chr_3 | g414 | g414.t1 | cds | g414.t1.CDS1 | 3278747 | 3279319 |
| chr_3 | g414 | g414.t1 | TSS | g414.t1 | NA | NA |
| chr_3 | g414 | g414.t1 | TTS | g414.t1 | NA | NA |
Sequences
>g414.t1 Gene=g414 Length=573
ATGGACAATAATAATAAATATATTTTTCTTATTTCAACAGTTTTTCATCATCAAAATGCA
GCAACTGCAGTAGAAAATCTTTCACCAATTAATGAATTGACAGAATTATCTTATGGAAAC
CTTCATTCACGTCATCATCAATCGATGCTTGAAAAGAATCGAAAATATTTTCAACATTTA
CAGCAACAACTTCATCATCAGCAACAGCAGCAGCAGCAAGCAGAAATATCAGCAAGATCA
GAATCATATCCATCAGATACAGAAGATGATCATGTAGATATTGAAGAAGATGATGAGAAT
GGTGAAATTATTGAAATGGATGATGATGAACATGAACATAATCATACAGGTGATAACTCG
ACTGGCACGAGTGGAATAATCACAAAGAAAAGAAAACGACGTGTGCTTTTTTCAAAGGCT
CAAACTTTTGAACTTGAAAGACGATTTAGACAGCAAAGATATTTGTCAGCACCTGAACGT
GAACATCTTGCATCACTTATTCGTCTAACACCGACACAAGTTAAAATTTGGTTCCAAAAT
CATCGTTATAAGACAAAAAAGAGCAGCTCATGA
>g414.t1 Gene=g414 Length=190
MDNNNKYIFLISTVFHHQNAATAVENLSPINELTELSYGNLHSRHHQSMLEKNRKYFQHL
QQQLHHQQQQQQQAEISARSESYPSDTEDDHVDIEEDDENGEIIEMDDDEHEHNHTGDNS
TGTSGIITKKRKRRVLFSKAQTFELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQN
HRYKTKKSSS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g414.t1 | CDD | cd00086 | homeodomain | 131 | 189 | 1.13716E-19 |
| 8 | g414.t1 | Gene3D | G3DSA:1.10.10.60 | - | 96 | 189 | 5.7E-24 |
| 12 | g414.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 59 | 92 | - |
| 14 | g414.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 59 | 81 | - |
| 13 | g414.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 127 | - |
| 2 | g414.t1 | PANTHER | PTHR24340:SF82 | HOMEOBOX PROTEIN VND | 34 | 188 | 4.6E-53 |
| 3 | g414.t1 | PANTHER | PTHR24340 | HOMEOBOX PROTEIN NKX | 34 | 188 | 4.6E-53 |
| 4 | g414.t1 | PRINTS | PR00024 | Homeobox signature | 152 | 163 | 5.1E-6 |
| 6 | g414.t1 | PRINTS | PR00024 | Homeobox signature | 167 | 177 | 5.1E-6 |
| 5 | g414.t1 | PRINTS | PR00024 | Homeobox signature | 177 | 186 | 5.1E-6 |
| 1 | g414.t1 | Pfam | PF00046 | Homeodomain | 131 | 187 | 9.5E-19 |
| 11 | g414.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 163 | 186 | - |
| 15 | g414.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 128 | 188 | 19.5 |
| 10 | g414.t1 | SMART | SM00389 | HOX_1 | 130 | 190 | 3.4E-17 |
| 7 | g414.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 115 | 187 | 8.98E-24 |
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:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0006355 | regulation of transcription, DNA-templated | 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. There were no conditions that were differentially expressed