General information for g4235.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein aristaless.
Parent gene
- The parent gene g4235 is located on chr_2: 514016..520564 (+ 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_2 | g4235 | g4235.t1 | isoform | g4235.t1 | 514016 | 520564 |
| chr_2 | g4235 | g4235.t1 | exon | g4235.t1.exon1 | 514016 | 514048 |
| chr_2 | g4235 | g4235.t1 | cds | g4235.t1.CDS1 | 514016 | 514048 |
| chr_2 | g4235 | g4235.t1 | exon | g4235.t1.exon2 | 519938 | 520564 |
| chr_2 | g4235 | g4235.t1 | cds | g4235.t1.CDS2 | 519938 | 520564 |
| chr_2 | g4235 | g4235.t1 | TTS | g4235.t1 | 520740 | 520740 |
| chr_2 | g4235 | g4235.t1 | TSS | g4235.t1 | NA | NA |
Sequences
>g4235.t1 Gene=g4235 Length=660
ATGAAAATTGGGTTAACAGAAGCAAGAATACAGGTTTGGTTTCAGAACAAAAGGGCAAAA
CATAGGAAACAAGAGAAAGTTGGGCCAGCTGGTCATCCATATAATGCTTATATGCCAACA
ATATCATCATCATCAGCAAGTGCTCTTCCATCAAATCCCTTTACTCATTTGGGATTTAAT
TTACGAAAACAATTTGATGCTGCAAGTTTGGCTGCATTTCGTTATCCACAATTGACAGCA
AACCCAATGATTCCATCGGCCTATTTCAATCAATTTCATCGTGCACCACCACCGCCTCTT
CTTCTTCATCATAGTGTTGGTGGACTTTATTCGCCTGCTAGTGCATCATTTCAGACACTT
CTAGCCAATATTTCAGCTGCTCAACGACCACCACCAATTCTTCCAACAATGCCTACCAAA
TCTTCTTCTGAATATATACCTGTAAGCTTAGCTTTGACTGTATCACCACCAATTTTCCAA
CTGATTCCAATAAGTCATCAACTTCAGCACCATTTAACACCAATTAATGTTTCATCACCT
GCTGCTGCTGCATCACATCAAAGTGCATTATCACCAAATGCAAACACCACCAGCTCAACA
CCACCACCTGAAGATCGTCGTAGCTCAATCTATTGCTGCATTACGCTTAAAAGCACGTGA
>g4235.t1 Gene=g4235 Length=219
MKIGLTEARIQVWFQNKRAKHRKQEKVGPAGHPYNAYMPTISSSSASALPSNPFTHLGFN
LRKQFDAASLAAFRYPQLTANPMIPSAYFNQFHRAPPPPLLLHHSVGGLYSPASASFQTL
LANISAAQRPPPILPTMPTKSSSEYIPVSLALTVSPPIFQLIPISHQLQHHLTPINVSSP
AAAASHQSALSPNANTTSSTPPPEDRRSSIYCCITLKST
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4235.t1 | CDD | cd00086 | homeodomain | 2 | 25 | 5.48449E-9 |
| 6 | g4235.t1 | Gene3D | G3DSA:1.10.10.60 | - | 1 | 28 | 6.1E-10 |
| 4 | g4235.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 183 | 206 | - |
| 5 | g4235.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 183 | 205 | - |
| 2 | g4235.t1 | PANTHER | PTHR24329 | HOMEOBOX PROTEIN ARISTALESS | 1 | 209 | 6.4E-15 |
| 1 | g4235.t1 | Pfam | PF00046 | Homeodomain | 2 | 23 | 1.4E-7 |
| 7 | g4235.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 1 | 24 | 11.451 |
| 3 | g4235.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 2 | 31 | 2.52E-9 |
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 |
KEGG
Orthology
- This transcript has been annotated with K09452 (homeobox protein aristaless-related)
Pathway
This gene does not belong to any 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