General information for g12720.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein ARX.
Parent gene
- The parent gene g12720 is located on chr_1: 25447533..25449611 (+ 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_1 | g12720 | g12720.t1 | TSS | g12720.t1 | 25446099 | 25446099 |
| chr_1 | g12720 | g12720.t1 | isoform | g12720.t1 | 25446598 | 25447533 |
| chr_1 | g12720 | g12720.t1 | exon | g12720.t1.exon1 | 25446598 | 25446623 |
| chr_1 | g12720 | g12720.t1 | cds | g12720.t1.CDS1 | 25446598 | 25446623 |
| chr_1 | g12720 | g12720.t1 | exon | g12720.t1.exon2 | 25446688 | 25446830 |
| chr_1 | g12720 | g12720.t1 | cds | g12720.t1.CDS2 | 25446688 | 25446830 |
| chr_1 | g12720 | g12720.t1 | exon | g12720.t1.exon3 | 25446887 | 25447533 |
| chr_1 | g12720 | g12720.t1 | cds | g12720.t1.CDS3 | 25446887 | 25447533 |
| chr_1 | g12720 | g12720.t1 | TTS | g12720.t1 | NA | NA |
Sequences
>g12720.t1 Gene=g12720 Length=816
ATGAAGAGAAAACAAAGAAGATATAGAACAACATTCAACAATTATCAACTGCAAGAACTT
GAAAGAGCTTTCATGCAGACACATTATCCTGATTGCTTTTTTAGAGAAGAACTGGCACTT
CGAATTGATTTAACAGAAGCTCGAGTGCAAGTTTGGTTTCAAAATAGAAGAGCAAAATGG
CGAAAGAGTGAAAGAATCGATGACAAAGAATATCAAGCAAATAATTGTTATGACTCTCAG
CAGCAACATCAGCATGAAGATATGCCATCAACTTCAAAATCAGTGTTACAAGAATGTGAA
ACACTTCAATCTGTACCACAACAACTTCAATCATCACATCCGTTGCAATGTGAACAAGAT
ACTTCAAAATTATTAAACAGTACTAACATATCCGATGATCGTCTCTCACCGAATCTTTTC
CTTAATTTAAATTTTGAAAATTCAAATACTCTAGACACAAATGTGAATGCATTAAAATTT
GAGTGGAGCAGTTTTAATCCAACAATTATCACACCAACAACTACAACTGTGCCTTCTATG
TCGATGTCACCAGTACCTTTACCTCATAGTAAATTTATATCATCACCCACATATGAATTT
CTTAATGTTGATCAGTTCAATATTGATAATTTTAAAAACGAATGCATTCTAAATCTTGAT
CATAATCTATTAAACTCAGTGAACGATACTTCATCGACAATTATTTCGAGTTCAATGCCA
ACACGTAGCATTGACTGCTTTTCATTAAGTGACGAAACTAAAGAATTACTTGATCTCGAG
AAACCAATTAACATAAATATAAACGATAAATATTGA
>g12720.t1 Gene=g12720 Length=271
MKRKQRRYRTTFNNYQLQELERAFMQTHYPDCFFREELALRIDLTEARVQVWFQNRRAKW
RKSERIDDKEYQANNCYDSQQQHQHEDMPSTSKSVLQECETLQSVPQQLQSSHPLQCEQD
TSKLLNSTNISDDRLSPNLFLNLNFENSNTLDTNVNALKFEWSSFNPTIITPTTTTVPSM
SMSPVPLPHSKFISSPTYEFLNVDQFNIDNFKNECILNLDHNLLNSVNDTSSTIISSSMP
TRSIDCFSLSDETKELLDLEKPINININDKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12720.t1 | CDD | cd00086 | homeodomain | 6 | 64 | 1.64348E-21 |
| 5 | g12720.t1 | Gene3D | G3DSA:1.10.10.60 | - | 1 | 68 | 2.7E-29 |
| 2 | g12720.t1 | PANTHER | PTHR24329 | HOMEOBOX PROTEIN ARISTALESS | 2 | 190 | 3.5E-46 |
| 3 | g12720.t1 | PANTHER | PTHR24329:SF543 | DORSAL ROOT GANGLIA HOMEOBOX | 2 | 190 | 3.5E-46 |
| 1 | g12720.t1 | Pfam | PF00046 | Homeodomain | 6 | 62 | 4.4E-22 |
| 7 | g12720.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 38 | 61 | - |
| 9 | g12720.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 3 | 63 | 20.358 |
| 8 | g12720.t1 | SMART | SM00389 | HOX_1 | 5 | 67 | 2.1E-24 |
| 4 | g12720.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 2 | 65 | 2.99E-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 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.
