General information for g8682.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Homeobox protein Nkx-2.1.
Parent gene
- The parent gene g8682 is located on chr_2: 32210288..32228259 (- 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_2 | g8682 | g8682.t2 | isoform | g8682.t2 | 32210288 | 32228259 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon1 | 32210288 | 32210695 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS1 | 32210288 | 32210695 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon2 | 32210759 | 32210845 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS2 | 32210759 | 32210845 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon3 | 32213493 | 32213588 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS3 | 32213493 | 32213588 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon4 | 32215831 | 32215985 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS4 | 32215831 | 32215985 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon5 | 32226989 | 32227209 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS5 | 32226989 | 32227209 |
| chr_2 | g8682 | g8682.t2 | exon | g8682.t2.exon6 | 32227997 | 32228259 |
| chr_2 | g8682 | g8682.t2 | cds | g8682.t2.CDS6 | 32227997 | 32228259 |
| chr_2 | g8682 | g8682.t2 | TSS | g8682.t2 | 32228612 | 32228612 |
| chr_2 | g8682 | g8682.t2 | TTS | g8682.t2 | NA | NA |
Sequences
>g8682.t2 Gene=g8682 Length=1230
ATGTCAGCCTCACTGGCAACAAACGCTGGAACATTTCCAGACGAAACCGAAACAGAACAA
GGTTTAACATTGCCCGATTTAAATGGCGTTGATTTGGTTATGAGCCTTTCTCCTAAAACC
AATCAACATTTACAACATTTACAAACGCTACAACAAAATTCATTGCATAATATCAATCAT
TCAACACCATTTTCAGTTACTGACATATTGAGTCCAATTGAAGAATATCGCAAGCTGGAA
TTAAATCCGCCTTCGCCTTACAGATCGAATTCGAGTGGATCTAGTGTTAATTCGCCAAGT
GCATTAGGAAATAGTGGTAATACTAATAATATGGCAAATCCATATGCAATGGGTCCACTT
TATCACAGCCCAGGCGTTCAAAGTTATTGCACGCCAACTGAAAATCTTTCACTTGCTGGA
CATTATACTGATATGAGAAGTTCAAGCTGGTATGGTTCAACTGCCAACGATCCACGTTTT
GCTATCACAAGGTTAATGGGAGGATCAGCTGGTAGCTCAATGGGACATGCAATGTCGAAC
ATGACTGGATTAGCAGCCTGCAATGTGAGTGATACAAAACCGATGCAATTTCCACTTACG
CAACGAAGAAAGCGACGAGTTCTATTCACACAAGCACAAGTTTATGAATTAGAAAGAAGA
TTTAAGCAACAAAAATACTTATCAGCACCTGAACGAGAGCATCTCGCCAGTTTAATTCAT
CTGACGCCTACACAAGTGAAAATCTGGTTCCAAAATCATCGTTATAAGTGCAAACGGCAA
GCAAAAGAGAAGGCAATGGCTGAACAAAATCAACATAATCAATCATCAAGCTCACCACGT
CGAGTAGCTGTTCCAGTATTAGTAAAAGACGGCAAGCCATGCTCTGGTAGCTCAAATTCG
ACACCTGTTCAACAGCAATTGACGTCAAGTGGTTCAACAATCGGCAACTCATCATCCAAT
ACAGTAAATTTAATTAATGTCGGTGGTGCAGGCGGCAGCGAATCGGCAACATCAAATAAT
CAGCATTCGCCAGTCGATTCTCCATCGACGACAATTTTGGGATATAATGGTAGTGGAGGA
CATCAACAAATGCTTCAGCAGCCGTGTAATAACACATTAATGTCCAATAGCCTTGCAATG
GCATATAGAAATCAAAATAATTTCATGGGCAATAGCCATCAACAGCAGCATTGCGGCAGT
TATCTTCCACTTCAGACGAGAGCTTGGTAA
>g8682.t2 Gene=g8682 Length=409
MSASLATNAGTFPDETETEQGLTLPDLNGVDLVMSLSPKTNQHLQHLQTLQQNSLHNINH
STPFSVTDILSPIEEYRKLELNPPSPYRSNSSGSSVNSPSALGNSGNTNNMANPYAMGPL
YHSPGVQSYCTPTENLSLAGHYTDMRSSSWYGSTANDPRFAITRLMGGSAGSSMGHAMSN
MTGLAACNVSDTKPMQFPLTQRRKRRVLFTQAQVYELERRFKQQKYLSAPEREHLASLIH
LTPTQVKIWFQNHRYKCKRQAKEKAMAEQNQHNQSSSSPRRVAVPVLVKDGKPCSGSSNS
TPVQQQLTSSGSTIGNSSSNTVNLINVGGAGGSESATSNNQHSPVDSPSTTILGYNGSGG
HQQMLQQPCNNTLMSNSLAMAYRNQNNFMGNSHQQQHCGSYLPLQTRAW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g8682.t2 | CDD | cd00086 | homeodomain | 203 | 260 | 3.1044E-23 |
| 8 | g8682.t2 | Gene3D | G3DSA:1.10.10.60 | - | 199 | 280 | 1.1E-24 |
| 12 | g8682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 21 | - |
| 15 | g8682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 260 | 319 | - |
| 14 | g8682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 281 | - |
| 13 | g8682.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 293 | 319 | - |
| 2 | g8682.t2 | PANTHER | PTHR24340:SF41 | MUSCLE-SPECIFIC HOMEOBOX PROTEIN TINMAN-RELATED | 45 | 319 | 3.2E-92 |
| 3 | g8682.t2 | PANTHER | PTHR24340 | HOMEOBOX PROTEIN NKX | 45 | 319 | 3.2E-92 |
| 4 | g8682.t2 | PRINTS | PR00024 | Homeobox signature | 224 | 235 | 3.5E-5 |
| 6 | g8682.t2 | PRINTS | PR00024 | Homeobox signature | 239 | 249 | 3.5E-5 |
| 5 | g8682.t2 | PRINTS | PR00024 | Homeobox signature | 249 | 258 | 3.5E-5 |
| 1 | g8682.t2 | Pfam | PF00046 | Homeodomain | 203 | 259 | 9.1E-20 |
| 11 | g8682.t2 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 235 | 258 | - |
| 16 | g8682.t2 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 200 | 260 | 19.742 |
| 10 | g8682.t2 | SMART | SM00389 | HOX_1 | 202 | 264 | 7.2E-25 |
| 7 | g8682.t2 | SUPERFAMILY | SSF46689 | Homeodomain-like | 179 | 262 | 2.22E-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 K09342 (homeobox protein Nkx-2.1)
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