General information for g6543.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Short stature homeobox protein 2.
Parent gene
- The parent gene g6543 is located on chr_2: 17557024..17563662 (- 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 | g6543 | g6543.t1 | isoform | g6543.t1 | 17557024 | 17563662 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon1 | 17557024 | 17557191 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS1 | 17557024 | 17557191 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon2 | 17557251 | 17557471 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS2 | 17557251 | 17557471 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon3 | 17560152 | 17560197 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS3 | 17560152 | 17560197 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon4 | 17560332 | 17560343 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS4 | 17560332 | 17560343 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon5 | 17561488 | 17561533 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS5 | 17561488 | 17561533 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon6 | 17561596 | 17561842 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS6 | 17561596 | 17561842 |
| chr_2 | g6543 | g6543.t1 | exon | g6543.t1.exon7 | 17563026 | 17563662 |
| chr_2 | g6543 | g6543.t1 | cds | g6543.t1.CDS7 | 17563026 | 17563662 |
| chr_2 | g6543 | g6543.t1 | TSS | g6543.t1 | 17563946 | 17563946 |
| chr_2 | g6543 | g6543.t1 | TTS | g6543.t1 | NA | NA |
Sequences
>g6543.t1 Gene=g6543 Length=1377
ATGGAGCAACTTGCTTATTTTGTGACAAAATCTTTTGAATATTCAAACACAACAAATCGT
GTGCTTGAAATTATAAAAATGTCAACTAAATTTGATGAGAAATCAGACAAAAGTGATTTG
AAAATTACTGATGAATCAATAAATGGTGATGATGACACTATGGATGGTTCAGTTGATATT
GACATAGACATCACAAATGACACTTCGAATGATGCAAAAATTTTGAGTGAACATGAGGAT
AAAAATGAAAATTGTGATAAAAAATCTAGTGATAAGACCAAAGAGAATACTTCTGAATTA
GTTGAAAGAACCGCAAGTCCTTTGCCATTAATTAAAAAATTAAATCGTGATGGTTCGAAA
CATGTGACAAAAAATTGGCTTATTTCAGATTGTCCTAAAAAGAAAATCAGTGAAACTACA
GATACAAAAGAATTCATTTCACCTCCCGAAAATCAAGAAAACGCTGCAATTAACTTGATT
CGTGTTGACGATTTGATTGGCAAAAAACAATCAATTGTACGTGCAAAACCTGTTAATGAG
TTATTAAAACAAATTAGAGAAATTAATAATCGATCGCCTTTAACAAAAAATGACAATTTT
AAAGTGGAAATTGTTGAGGATGCAAAAATAAAAACAGATAAAATTGAATCATCTGAGAAA
ATTGAAAGTGACCTCAATGATATAAAAGATGACAATATACATTCAAACTCAAGCGATAGT
AATGTTCTTCAACTTCTTAAATCACCATCATCGCCTAATGCTTCATTGAGTGGAAATTGC
AACAATAATAAGCAAAGAAGATCAAGGACGAATTTTACGTTAGAACAATTGAATGAATTA
GAGAGACTTTTTGAGGAAACGCATTATCCAGATGCATTTATGAGAGAGGAACTCAGTCAA
CGACTCAATCTTAGCGAAGCTCGTGTTCAAGTCTGGTTTCAGAATAGAAGAGCAAAATGC
AGAAAAGCAGAGAATCAATTACACAAAGGGATTTTAATAACAAATCATAGCAATAGCAGT
TCGATGACATCACCTATTGAATCATGTCGTGTTGCGCCATATGTAAATGTTCCTACCAAT
TTAAGACAGGTATCAGTCTCATCTGCAAGTGTCATCACAACTTCAAGTGTTTCTTCTACT
GTTACAACTTTCCCTTCAGTCGCCTCATTTTCTGCTTTCGATCCAACATTGCTTACTGCT
GCACATCAATATGCTGCTGCAATAACTGCAAGTGCAACTTTGGACAGAAGTCTTTTTACA
TTACCACAGTATCCACTTAATTTGGCAACAGCATTAGCAGCTCATAATAAAAACTCAAGT
ATAGCTGATCTTCGTCTAAAGGCTAAAAATTACGTAGAAGCTCTTGGCATAGAATAA
>g6543.t1 Gene=g6543 Length=458
MEQLAYFVTKSFEYSNTTNRVLEIIKMSTKFDEKSDKSDLKITDESINGDDDTMDGSVDI
DIDITNDTSNDAKILSEHEDKNENCDKKSSDKTKENTSELVERTASPLPLIKKLNRDGSK
HVTKNWLISDCPKKKISETTDTKEFISPPENQENAAINLIRVDDLIGKKQSIVRAKPVNE
LLKQIREINNRSPLTKNDNFKVEIVEDAKIKTDKIESSEKIESDLNDIKDDNIHSNSSDS
NVLQLLKSPSSPNASLSGNCNNNKQRRSRTNFTLEQLNELERLFEETHYPDAFMREELSQ
RLNLSEARVQVWFQNRRAKCRKAENQLHKGILITNHSNSSSMTSPIESCRVAPYVNVPTN
LRQVSVSSASVITTSSVSSTVTTFPSVASFSAFDPTLLTAAHQYAAAITASATLDRSLFT
LPQYPLNLATALAAHNKNSSIADLRLKAKNYVEALGIE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g6543.t1 | CDD | cd00086 | homeodomain | 266 | 324 | 2.58565E-24 |
| 5 | g6543.t1 | Gene3D | G3DSA:1.10.10.60 | - | 251 | 326 | 5.9E-30 |
| 9 | g6543.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 75 | 103 | - |
| 11 | g6543.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 75 | 99 | - |
| 10 | g6543.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 248 | 268 | - |
| 3 | g6543.t1 | PANTHER | PTHR46255 | SHORT STATURE HOMEOBOX | 1 | 456 | 4.6E-68 |
| 2 | g6543.t1 | Pfam | PF00046 | Homeodomain | 266 | 322 | 6.0E-24 |
| 1 | g6543.t1 | Pfam | PF03826 | OAR motif | 435 | 449 | 6.2E-6 |
| 7 | g6543.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 298 | 321 | - |
| 12 | g6543.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 263 | 323 | 21.135 |
| 8 | g6543.t1 | SMART | SM00389 | HOX_1 | 265 | 327 | 1.5E-27 |
| 4 | g6543.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 249 | 323 | 6.84E-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: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 K09331 (short stature homeobox protein)
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.
