General information for g1876.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeotic protein labial.
Parent gene
- The parent gene g1876 is located on chr_3: 13596110..13607402 (+ 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 | g1876 | g1876.t1 | TSS | g1876.t1 | 13595867 | 13595867 |
| chr_3 | g1876 | g1876.t1 | isoform | g1876.t1 | 13596110 | 13607402 |
| chr_3 | g1876 | g1876.t1 | exon | g1876.t1.exon1 | 13596110 | 13597043 |
| chr_3 | g1876 | g1876.t1 | cds | g1876.t1.CDS1 | 13596110 | 13597043 |
| chr_3 | g1876 | g1876.t1 | exon | g1876.t1.exon2 | 13606847 | 13606933 |
| chr_3 | g1876 | g1876.t1 | cds | g1876.t1.CDS2 | 13606847 | 13606933 |
| chr_3 | g1876 | g1876.t1 | exon | g1876.t1.exon3 | 13606996 | 13607162 |
| chr_3 | g1876 | g1876.t1 | cds | g1876.t1.CDS3 | 13606996 | 13607162 |
| chr_3 | g1876 | g1876.t1 | exon | g1876.t1.exon4 | 13607229 | 13607402 |
| chr_3 | g1876 | g1876.t1 | cds | g1876.t1.CDS4 | 13607229 | 13607402 |
| chr_3 | g1876 | g1876.t1 | TTS | g1876.t1 | 13607965 | 13607965 |
Sequences
>g1876.t1 Gene=g1876 Length=1362
ATGATGGACATTAGTATGTATGGAAATCATCATGCTAATCATTCGAGTGGATTTCAAAAT
CCTGATATAGGTACAGGTGGATATTCATATTTTTCATCATCTGGCCATCATCATCACCAT
CACATACAAAATCATCAAAGTCAAGCGTATGCAAATGCAAGTGGATTGCAACAGACGAGT
GGCAATGGCAGCAATGGATCAAATCACTTTTATTCATCTGCTATTGCAACTCATCCGCAT
CTGTACAGTCCAACTGCTATAGAATATGGAATTCATACCTCATCATCTAACAATTCACCC
GATCAATATTATGATGCTCAAAGTAATGAAGGTTACTATGTGACTACCAATGGCACTGCA
ACAAATAATAATAATAACAGCTCTAGCAATAATAACAATACTAGCAGCTCACCTGAGACT
CACATCATTAGCTCAGATAATGGCTTAAGCTATACAAATTTGGACTATATCGCTTATCAG
CAAGCTGCAGCAGCTCATCATAATCAAACACAGGGATATAATATTTCAATTCAGGGAGGT
GACGATAAATTGGCCATAACGCATCATTATAATGAAGAATTGCTGCTAAACAGCCACCAG
CATCATCAACATGCCACTCATCATCATAATCATAATGCGACAACAGCTAACCCATGGCAT
CATCCAAATACAAGCAATCATAATTTTATGGAAGCCAATGTTGGTCTGGTAAATCAGATG
CAAGCAATAAGCAGCAACAATTTGACACCGCAATCACAAATTCAAATTCAGCATGCCATG
CACTCGCCAAACAGTATTCAATCGTCATCATCACCCACGCTGCAAAGTCAACAACAGCAA
TCACAGGATTCACAAAATCAACAACAGCAGCAAGCTCAAAATGTACCGACCTATAAATGG
ATGCAAGTGAAACGAAATGTGCCAAAACCACAAACACCTAAGATCGCTGCAACTATGGAT
TATTCAGCAGTTCCATCTTCAATTGATCCCTGCCGACCAGGTATCTTTAATAGTTTGATG
GATCCTAATAACTTTAATTTGGCAGCAGCGGGAAGTAACAACACGGGTAGAACGAATTTT
ACAAATAAGCAGCTGACTGAGCTCGAAAAAGAATTTCATTTCAACAAATACCTCACACGA
GCGCGAAGAATTGAAATTGCAAATGCACTTCAACTTAATGAAACACAAGTGAAAATTTGG
TTTCAAAATCGTCGTATGAAGTTCAAAAAGCGAGTGAAGGAAGGCCTTATACCACCTGAA
TCACTCAGCCAGTCTCCAAAGAACTCTAGCACAGGCGCAAATGCAAGTGGTGATCAAACA
AATCTTGCCGGTAGCTGCGAAAACAGTAGAGAATCTAATTAG
>g1876.t1 Gene=g1876 Length=453
MMDISMYGNHHANHSSGFQNPDIGTGGYSYFSSSGHHHHHHIQNHQSQAYANASGLQQTS
GNGSNGSNHFYSSAIATHPHLYSPTAIEYGIHTSSSNNSPDQYYDAQSNEGYYVTTNGTA
TNNNNNSSSNNNNTSSSPETHIISSDNGLSYTNLDYIAYQQAAAAHHNQTQGYNISIQGG
DDKLAITHHYNEELLLNSHQHHQHATHHHNHNATTANPWHHPNTSNHNFMEANVGLVNQM
QAISSNNLTPQSQIQIQHAMHSPNSIQSSSSPTLQSQQQQSQDSQNQQQQQAQNVPTYKW
MQVKRNVPKPQTPKIAATMDYSAVPSSIDPCRPGIFNSLMDPNNFNLAAAGSNNTGRTNF
TNKQLTELEKEFHFNKYLTRARRIEIANALQLNETQVKIWFQNRRMKFKKRVKEGLIPPE
SLSQSPKNSSTGANASGDQTNLAGSCENSRESN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1876.t1 | CDD | cd00086 | homeodomain | 357 | 411 | 2.12936E-24 |
| 13 | g1876.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 121 | 140 | - |
| 12 | g1876.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 255 | 297 | - |
| 14 | g1876.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 413 | 453 | - |
| 11 | g1876.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 421 | 453 | - |
| 2 | g1876.t1 | PANTHER | PTHR45946:SF4 | HOMEOBOX PROTEIN ROUGH-RELATED | 1 | 436 | 2.0E-80 |
| 3 | g1876.t1 | PANTHER | PTHR45946 | HOMEOBOX PROTEIN ROUGH-RELATED | 1 | 436 | 2.0E-80 |
| 4 | g1876.t1 | PRINTS | PR00024 | Homeobox signature | 375 | 386 | 8.3E-8 |
| 6 | g1876.t1 | PRINTS | PR00024 | Homeobox signature | 390 | 400 | 8.3E-8 |
| 5 | g1876.t1 | PRINTS | PR00024 | Homeobox signature | 400 | 409 | 8.3E-8 |
| 1 | g1876.t1 | Pfam | PF00046 | Homeodomain | 356 | 410 | 1.9E-21 |
| 9 | g1876.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 386 | 409 | - |
| 15 | g1876.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 351 | 411 | 20.698 |
| 10 | g1876.t1 | SMART | SM00389 | HOX_1 | 353 | 415 | 3.0E-25 |
| 7 | g1876.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 340 | 411 | 1.71E-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 K09301 (homeobox protein HoxA/B/D1)
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. There were no conditions that were differentially expressed