General information for g4031.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homeotic protein Sex combs reduced.
Parent gene
- The parent gene g4031 is located on chr_3: 29703222..29724261 (- 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 | g4031 | g4031.t1 | isoform | g4031.t1 | 29703222 | 29724261 |
| chr_3 | g4031 | g4031.t1 | exon | g4031.t1.exon1 | 29703222 | 29703363 |
| chr_3 | g4031 | g4031.t1 | cds | g4031.t1.CDS1 | 29703222 | 29703363 |
| chr_3 | g4031 | g4031.t1 | exon | g4031.t1.exon2 | 29703429 | 29703594 |
| chr_3 | g4031 | g4031.t1 | cds | g4031.t1.CDS2 | 29703429 | 29703594 |
| chr_3 | g4031 | g4031.t1 | exon | g4031.t1.exon3 | 29722519 | 29722566 |
| chr_3 | g4031 | g4031.t1 | cds | g4031.t1.CDS3 | 29722519 | 29722566 |
| chr_3 | g4031 | g4031.t1 | exon | g4031.t1.exon4 | 29723583 | 29724261 |
| chr_3 | g4031 | g4031.t1 | cds | g4031.t1.CDS4 | 29723583 | 29724261 |
| chr_3 | g4031 | g4031.t1 | TSS | g4031.t1 | NA | NA |
| chr_3 | g4031 | g4031.t1 | TTS | g4031.t1 | NA | NA |
Sequences
>g4031.t1 Gene=g4031 Length=1035
ATGGATGCAAATAATTTTGTCATGTCATCATACCAATTTGTAAATTCACTTGCACAATGT
TATCCAAATAACTCAAGCAACACATCGAATAGTACAAGTAGTAATGGGCCACAGAATGAC
TACTTTCCAGGCTCAGCCTACAATCCAAATCTTTATTCAGGCGCCCCGCAATCACATTAT
CCCAATCCACAGTCCTATAATCCTCTAACAGCAGCAACAGCAAGCTCACAGCAGCCAGGC
AATGGCGGTGATATGGTTGATTATACACAACTGCAGCCACAAAAGTTTATGCTTAATCAA
CAGCAAGCACTGGGACAGGCGAGTTGCAAATATGCGGGCGATGGGCAGGGCACGCCAAAT
ATCAATCAAACCTCTATATCTAGCCCTCAAGATTTGTCGACTGCTCGTGATATTTCGCCC
AAGTTATCGCCAAGTTCGGTCGTGGACAATGCAGCACGCTCAATGAACAAACAACAGCAA
CAACAACAACATTCAACAAATAATAATAATAACAATATAGCGAATAATAATAGTAAATCC
AATAATAGCAGTGCTAATACAAATAGCAGTCATCTTCAATCGACATCACTGCCAATGCGC
AGTCCCGATGGCGATGAATCTGATGCATCCAGTGATAGTGGAACTGAAGGTGGCAGCGGT
ACTGGCAGTGGTAAGAAAAATCCACCACAAATCTACCCATGGATGAAGAGGGTACATTTA
GGACAAAGTACAGTGAATGCAAATGGCGAGACCAAGAGACAACGTACTTCATATACACGC
TATCAGACGCTAGAATTAGAAAAGGAATTTCATTTCAATCGCTATTTGACGCGTCGACGA
CGAATTGAAATTGCTCATGCATTATGCTTGACTGAACGCCAAATTAAAATTTGGTTCCAA
AATCGTCGTATGAAATGGAAGAAAGAACATAAAATGGCATCAATGAATATCGTGCCATAT
CATATGTCACCTTATGGTCATCCATACGCTCAATTTGATATCCATCCTAGCCAATTTGCG
CATCTCTCGGCCTAG
>g4031.t1 Gene=g4031 Length=344
MDANNFVMSSYQFVNSLAQCYPNNSSNTSNSTSSNGPQNDYFPGSAYNPNLYSGAPQSHY
PNPQSYNPLTAATASSQQPGNGGDMVDYTQLQPQKFMLNQQQALGQASCKYAGDGQGTPN
INQTSISSPQDLSTARDISPKLSPSSVVDNAARSMNKQQQQQQHSTNNNNNNIANNNSKS
NNSSANTNSSHLQSTSLPMRSPDGDESDASSDSGTEGGSGTGSGKKNPPQIYPWMKRVHL
GQSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ
NRRMKWKKEHKMASMNIVPYHMSPYGHPYAQFDIHPSQFAHLSA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g4031.t1 | CDD | cd00086 | homeodomain | 252 | 310 | 3.70536E-25 |
| 10 | g4031.t1 | Gene3D | G3DSA:1.10.10.60 | - | 226 | 311 | 1.5E-33 |
| 15 | g4031.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 228 | - |
| 16 | g4031.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 201 | - |
| 17 | g4031.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 211 | 226 | - |
| 2 | g4031.t1 | PANTHER | PTHR45771:SF11 | HOMEOTIC PROTEIN SEX COMBS REDUCED | 4 | 344 | 5.1E-125 |
| 3 | g4031.t1 | PANTHER | PTHR45771 | HOMEOTIC PROTEIN DEFORMED | 4 | 344 | 5.1E-125 |
| 8 | g4031.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 230 | 237 | 7.6E-6 |
| 7 | g4031.t1 | PRINTS | PR00025 | Homeotic antennapedia protein signature | 252 | 267 | 7.6E-6 |
| 6 | g4031.t1 | PRINTS | PR00024 | Homeobox signature | 273 | 284 | 7.7E-9 |
| 5 | g4031.t1 | PRINTS | PR00024 | Homeobox signature | 288 | 298 | 7.7E-9 |
| 4 | g4031.t1 | PRINTS | PR00024 | Homeobox signature | 298 | 307 | 7.7E-9 |
| 1 | g4031.t1 | Pfam | PF00046 | Homeodomain | 252 | 308 | 1.6E-21 |
| 14 | g4031.t1 | ProSitePatterns | PS00032 | ‘Homeobox’ antennapedia-type protein signature. | 231 | 236 | - |
| 13 | g4031.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 284 | 307 | - |
| 18 | g4031.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 249 | 309 | 21.767 |
| 12 | g4031.t1 | SMART | SM00389 | HOX_1 | 251 | 313 | 4.5E-26 |
| 9 | g4031.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 233 | 309 | 5.13E-26 |
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 K09305 (homeobox protein HoxA/B/C5)
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