General information for g4004.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein aristaless-like 3.
Parent gene
- The parent gene g4004 is located on chr_3: 29479620..29480541 (- 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 | g4004 | g4004.t1 | TTS | g4004.t1 | 29479340 | 29479340 |
| chr_3 | g4004 | g4004.t1 | isoform | g4004.t1 | 29479620 | 29480541 |
| chr_3 | g4004 | g4004.t1 | exon | g4004.t1.exon1 | 29479620 | 29479936 |
| chr_3 | g4004 | g4004.t1 | cds | g4004.t1.CDS1 | 29479620 | 29479936 |
| chr_3 | g4004 | g4004.t1 | exon | g4004.t1.exon2 | 29480007 | 29480092 |
| chr_3 | g4004 | g4004.t1 | cds | g4004.t1.CDS2 | 29480007 | 29480092 |
| chr_3 | g4004 | g4004.t1 | exon | g4004.t1.exon3 | 29480180 | 29480194 |
| chr_3 | g4004 | g4004.t1 | cds | g4004.t1.CDS3 | 29480180 | 29480194 |
| chr_3 | g4004 | g4004.t1 | exon | g4004.t1.exon4 | 29480275 | 29480337 |
| chr_3 | g4004 | g4004.t1 | cds | g4004.t1.CDS4 | 29480275 | 29480337 |
| chr_3 | g4004 | g4004.t1 | exon | g4004.t1.exon5 | 29480393 | 29480541 |
| chr_3 | g4004 | g4004.t1 | cds | g4004.t1.CDS5 | 29480393 | 29480541 |
| chr_3 | g4004 | g4004.t1 | TSS | g4004.t1 | NA | NA |
Sequences
>g4004.t1 Gene=g4004 Length=630
ATGGCAAGTCCTTTTTTAACTTTATTACCAAGTGAATTATTAACAGATTATATGTTTGGT
CGAAGGAGACAGAGAAGAAATAGAACAACATTTAATTCACGACAACTCGAAGAATTAGAA
TCTCTCTTTAAACAAACACATTACCCAGATGTCTTTTTGAGAGAGGAAATTGCATTGAGA
ATAAGTCTTAGTGAAGCAAGAGTTCAAGTTTGGTTTCAAAATCGCAGGGCAAAGTGGCGT
AAACAAACACGATTTCAACTTATACAAGATGCATGGCGTATGAGACTCAATGAAATTAAT
CCAACAGCAATAACCACAAAAACAGATATCTCTAAATCACCATCATCGGCAGCATATGAA
AAATTTATTTGTGAAAATGTAATAAAGAGTTCTGAGAAATTTGAACAATCAGAAAGTGGT
GTTGTTGTTGGTAGTAGAAAGAATGTAGTACCGAATGAAAACGAAATTATGTTGTATAAA
AATAACAAAAAGGACCTGTGTGAGAGTGACGATGACAAAGATGAATCAGAATCAGAAATT
GATTTAGTCACAACTACAAGAAGTTCGCAAGACAATTCATTCGCACTCGATTTCTCAAAT
AATAACAATAATAATATTAGTGATAAATAA
>g4004.t1 Gene=g4004 Length=209
MASPFLTLLPSELLTDYMFGRRRQRRNRTTFNSRQLEELESLFKQTHYPDVFLREEIALR
ISLSEARVQVWFQNRRAKWRKQTRFQLIQDAWRMRLNEINPTAITTKTDISKSPSSAAYE
KFICENVIKSSEKFEQSESGVVVGSRKNVVPNENEIMLYKNNKKDLCESDDDKDESESEI
DLVTTTRSSQDNSFALDFSNNNNNNISDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4004.t1 | CDD | cd00086 | homeodomain | 29 | 82 | 5.98088E-20 |
| 5 | g4004.t1 | Gene3D | G3DSA:1.10.10.60 | - | 18 | 89 | 1.4E-28 |
| 10 | g4004.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 167 | 209 | - |
| 9 | g4004.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 182 | 209 | - |
| 2 | g4004.t1 | PANTHER | PTHR24329:SF538 | IP01065P | 1 | 131 | 1.7E-61 |
| 3 | g4004.t1 | PANTHER | PTHR24329 | HOMEOBOX PROTEIN ARISTALESS | 1 | 131 | 1.7E-61 |
| 1 | g4004.t1 | Pfam | PF00046 | Homeodomain | 25 | 81 | 1.1E-22 |
| 7 | g4004.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 57 | 80 | - |
| 11 | g4004.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 22 | 82 | 20.698 |
| 8 | g4004.t1 | SMART | SM00389 | HOX_1 | 24 | 86 | 2.6E-24 |
| 4 | g4004.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 9 | 82 | 8.13E-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: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