General information for g13158.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeobox protein extradenticle.
Parent gene
- The parent gene g13158 is located on chr_1: 28286048..28287831 (- 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 | g13158 | g13158.t1 | TTS | g13158.t1 | 28285238 | 28285238 |
| chr_1 | g13158 | g13158.t1 | isoform | g13158.t1 | 28285525 | 28286920 |
| chr_1 | g13158 | g13158.t1 | exon | g13158.t1.exon1 | 28285525 | 28285963 |
| chr_1 | g13158 | g13158.t1 | cds | g13158.t1.CDS1 | 28285525 | 28285963 |
| chr_1 | g13158 | g13158.t1 | exon | g13158.t1.exon2 | 28286023 | 28286133 |
| chr_1 | g13158 | g13158.t1 | cds | g13158.t1.CDS2 | 28286023 | 28286133 |
| chr_1 | g13158 | g13158.t1 | exon | g13158.t1.exon3 | 28286220 | 28286394 |
| chr_1 | g13158 | g13158.t1 | cds | g13158.t1.CDS3 | 28286220 | 28286394 |
| chr_1 | g13158 | g13158.t1 | exon | g13158.t1.exon4 | 28286521 | 28286920 |
| chr_1 | g13158 | g13158.t1 | cds | g13158.t1.CDS4 | 28286521 | 28286920 |
| chr_1 | g13158 | g13158.t1 | TSS | g13158.t1 | 28287918 | 28287918 |
Sequences
>g13158.t1 Gene=g13158 Length=1125
ATGGAAGATCCAAATCGTATGATGGCTCATGCAGCATCAAATCCTTCATACGCACAGCCA
TATGGTATGCCAAGTGATTCGCAATCGGTTGGTGATGACCCACGAAAGCAGGACATTGGT
GAAATTCTTCAACAAATTATGAACATCACTGATCAATCACTTGATGAAGCACAAGCTCGA
AAGCACACACTTAATTGTCATCGCATGAAGCCGGTTCTTTTTGCAGTGCTCTGTGAGATC
AAGGAGAAAACAGTATTGTCATTACGCAATACTCAAGAGGAAGAACCTCCAGATCCTCAA
CTCATGCGTTTAGATAACATGCTTATTGCAGAAGGTGTTGCTGGTCCCGAAAAAGGCGGC
GGTGCAGGAGCAGCAGCTTCTGCTTCAGCGGCCGCATCAGAGGACTTTGGTGACATGGGC
AGTGGTCAGGACAATGCTATTGAGCATTCTGACTACCGCGCCAAATTGGCTCAAATTCGT
CAAATTTATCATCAAGAACTCGAAAAATATGAACAAGCATGCAGTGAATTTACAACACAC
GTTATGAATCTGCTACGTGAACAGAGTAGAACACGCCCCATTACACCGAAAGAAATTGAA
CGAATGGTACAGATTATTCACAAGAAATTCAGCTCGATTCAAATGCAGTTAAAACAATCT
ACTTGCGAAGCTGTCATGATTTTGAGATCACGATTTTTGGATGCTCGTCGCAAGCGAAGA
AACTTTAGTAAACAAGCTTCCGAAATTCTCAATGAATATTTCTATAGCCACCTTAGCAAT
CCTTATCCATCAGAAGAGGCAAAAGAGGATTTAGCTCGAAAATGTGGCATCACTGTCTCT
CAAGTATCCAACTGGTTTGGAAATAAACGCATTCGTTACAAGAAGAATATTGGCAAAGCA
CAGGAGGAAGCAAATCTTTATGCAGCAAAGAAGGCAGCTGGTGCCAGTCCATATTCTATG
GCAGGCCCTCCTTCAGGTGCTACAACACCAATGATGAGTCCAGCACCTGCACAAGATTCA
ATGGGATATTCACTCGGATCAGGTGGTTACGATCAACAGCAAGCATATGATGGCAGTATG
GGTGGATACGATATGCATCAAGGTAAAGATCGTGATGACTTTTGA
>g13158.t1 Gene=g13158 Length=374
MEDPNRMMAHAASNPSYAQPYGMPSDSQSVGDDPRKQDIGEILQQIMNITDQSLDEAQAR
KHTLNCHRMKPVLFAVLCEIKEKTVLSLRNTQEEEPPDPQLMRLDNMLIAEGVAGPEKGG
GAGAAASASAAASEDFGDMGSGQDNAIEHSDYRAKLAQIRQIYHQELEKYEQACSEFTTH
VMNLLREQSRTRPITPKEIERMVQIIHKKFSSIQMQLKQSTCEAVMILRSRFLDARRKRR
NFSKQASEILNEYFYSHLSNPYPSEEAKEDLARKCGITVSQVSNWFGNKRIRYKKNIGKA
QEEANLYAAKKAAGASPYSMAGPPSGATTPMMSPAPAQDSMGYSLGSGGYDQQQAYDGSM
GGYDMHQGKDRDDF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13158.t1 | CDD | cd00086 | homeodomain | 236 | 296 | 1.17596E-17 |
| 6 | g13158.t1 | Gene3D | G3DSA:1.10.10.60 | - | 234 | 309 | 1.7E-31 |
| 11 | g13158.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 33 | - |
| 10 | g13158.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 355 | 374 | - |
| 3 | g13158.t1 | PANTHER | PTHR11850:SF50 | PRE-B-CELL LEUKEMIA TRANSCRIPTION FACTOR 2 | 15 | 322 | 5.4E-179 |
| 4 | g13158.t1 | PANTHER | PTHR11850 | HOMEOBOX PROTEIN TRANSCRIPTION FACTORS | 15 | 322 | 5.4E-179 |
| 1 | g13158.t1 | Pfam | PF03792 | PBC domain | 36 | 234 | 2.4E-92 |
| 2 | g13158.t1 | Pfam | PF00046 | Homeodomain | 236 | 295 | 1.2E-18 |
| 8 | g13158.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 271 | 294 | - |
| 12 | g13158.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 233 | 296 | 17.07 |
| 9 | g13158.t1 | SMART | SM00389 | HOX_1 | 235 | 300 | 3.4E-17 |
| 5 | g13158.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 235 | 303 | 5.56E-20 |
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 transcript has been annotated with K09355 (pre-B-cell leukemia transcription factor 1)
Pathway
- This transcript belongs to the following 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.
