General information for g2018.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeobox protein homothorax.
Parent gene
- The parent gene g2018 is located on chr_3: 14491789..14527043 (+ 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 | g2018 | g2018.t1 | isoform | g2018.t1 | 14491789 | 14527043 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon1 | 14491789 | 14491834 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS1 | 14491789 | 14491834 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon2 | 14491905 | 14492003 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS2 | 14491905 | 14492003 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon3 | 14507492 | 14507640 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS3 | 14507492 | 14507640 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon4 | 14513233 | 14513309 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS4 | 14513233 | 14513309 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon5 | 14523464 | 14523522 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS5 | 14523464 | 14523522 |
| chr_3 | g2018 | g2018.t1 | exon | g2018.t1.exon6 | 14526892 | 14527043 |
| chr_3 | g2018 | g2018.t1 | cds | g2018.t1.CDS6 | 14526892 | 14527043 |
| chr_3 | g2018 | g2018.t1 | TTS | g2018.t1 | 14527504 | 14527504 |
| chr_3 | g2018 | g2018.t1 | TSS | g2018.t1 | NA | NA |
Sequences
>g2018.t1 Gene=g2018 Length=582
ATGTGTTTGTTTTTCTGGTTTTGGACTCTCCTTATAGAATCATCATCACGATGGTGTCGA
AGAGAATGGTCATCCCCTCCAGATACACGAGCGAACGACCCGTCAAGGCGCGTCCTATAC
TCTTCAGTCTTCCTAGGCAGTCCCGGTGATGCCAGCAATGCGAGTGTGGGGTCCGGCGAA
GGAACGGGCGAGGAGGATGACGATACGAACGGAAAAAAGAATCAAAAGAAACGTGGCATA
TTTCCAAAAGTGGCAACAAATATCCTTAGAGCGTGGCTCTTTCAACATCTAACGCATCCC
TATCCTTCAGAAGACCAGAAAAAACAATTAGCACAAGATACTGGTTTAACGATATTACAA
GTAAATAATTGGTTTATTAATGCTAGACGGAGAATTGTACAACCAATGATTGACCAATCA
AATAGAGCAGTATACACGCATCCGGGTCCAAGCGGTGGCTATCCCGATCCAATGAGCTAT
ATGATGGAAGGCAATCAAATGATGCATCGACCACCAGGCGATCCAGGATTCCATCAAGGT
TATCATTATCCACCTGCCGAATATTATCCTCATCATTTGTAA
>g2018.t1 Gene=g2018 Length=193
MCLFFWFWTLLIESSSRWCRREWSSPPDTRANDPSRRVLYSSVFLGSPGDASNASVGSGE
GTGEEDDDTNGKKNQKKRGIFPKVATNILRAWLFQHLTHPYPSEDQKKQLAQDTGLTILQ
VNNWFINARRRIVQPMIDQSNRAVYTHPGPSGGYPDPMSYMMEGNQMMHRPPGDPGFHQG
YHYPPAEYYPHHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g2018.t1 | CDD | cd00086 | homeodomain | 76 | 131 | 3.14201E-15 |
| 6 | g2018.t1 | Gene3D | G3DSA:1.10.10.60 | - | 77 | 143 | 9.0E-40 |
| 14 | g2018.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 50 | 79 | - |
| 2 | g2018.t1 | PANTHER | PTHR11850 | HOMEOBOX PROTEIN TRANSCRIPTION FACTORS | 48 | 174 | 7.7E-55 |
| 3 | g2018.t1 | PANTHER | PTHR11850:SF126 | HOMEOBOX PROTEIN MEIS1 | 48 | 174 | 7.7E-55 |
| 1 | g2018.t1 | Pfam | PF05920 | Homeobox KN domain | 92 | 131 | 2.7E-20 |
| 8 | g2018.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 16 | - |
| 9 | g2018.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 10 | g2018.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 12 | - |
| 11 | g2018.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 16 | - |
| 7 | g2018.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 17 | 193 | - |
| 15 | g2018.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 72 | 135 | 13.54 |
| 13 | g2018.t1 | SMART | SM00389 | HOX_1 | 74 | 139 | 2.8E-12 |
| 4 | g2018.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 73 | 148 | 8.98E-21 |
| 5 | g2018.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 16 | - |
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: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