General information for g10056.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative GS homeobox 2.
Parent gene
- The parent gene g10056 is located on chr_1: 7119498..7120384 (- 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_1 | g10056 | g10056.t1 | isoform | g10056.t1 | 7119498 | 7120384 |
| chr_1 | g10056 | g10056.t1 | exon | g10056.t1.exon1 | 7119498 | 7119648 |
| chr_1 | g10056 | g10056.t1 | cds | g10056.t1.CDS1 | 7119498 | 7119648 |
| chr_1 | g10056 | g10056.t1 | exon | g10056.t1.exon2 | 7119747 | 7120384 |
| chr_1 | g10056 | g10056.t1 | cds | g10056.t1.CDS2 | 7119747 | 7120384 |
| chr_1 | g10056 | g10056.t1 | TSS | g10056.t1 | NA | NA |
| chr_1 | g10056 | g10056.t1 | TTS | g10056.t1 | NA | NA |
Sequences
>g10056.t1 Gene=g10056 Length=789
ATGTCTCGATCATTTTTAGTGGATTCACTTATTAGTGATAAATGTAATTCTAAACCAGTG
AAAAGTGAAATATTACCACCTCAAACAATTATCACTACACCACAATCAAATCCTTATTCA
CCATCATATATTGGAAGTTATTTATTTTCTCTGAGTTTACAACAACAGCAGCATCAACAA
ATGCTTCAACGTCATTATCAATCACCACAACGCGATCAATTATTGGATTTAACAACTCCC
AAGCCATATATTCCCACTAATTTACCGCCGATTTTTGTGCCAACATCGACAAACTTTTAC
GAGCGTGCTCTTATTTTGAAAAATTCACCAACATCAAGACATGAAGTGTCACAATCACGT
TCACCGTCGGCTTCACCTCCAATAAAGAGAAATTTATATGCACCATATGATTTGAGCGAT
AGACCCATGCACTCACAGTCACCAAAATCAAATTCTCCATCGCCTACGCCAACACATTAT
GACTCTGATTCTTCAAGTAAACGAATTCGTACAGCTTTTTCGAGTACACAACTTTTGGAT
TTAGAACGCGAATTCTCGGCAAATCAATACTTGACACGTTTAAGACGCATTGAAATAGCA
ACGCGCCTTAAGCTGTCAGAAAAGCAAGTGAAAATATGGTTTCAAAACAGACGCGTTAAG
TATAAGAAAGATGATTGTCCTAATGCAAGCAGTGAACAACAACAGCAACTAATTCATGCT
CATGGAAGTGTCAGTAGTGGCAGTTGTACGAACTGTAAATGCAGTAATTCACAACCATCA
TTAGTGTAA
>g10056.t1 Gene=g10056 Length=262
MSRSFLVDSLISDKCNSKPVKSEILPPQTIITTPQSNPYSPSYIGSYLFSLSLQQQQHQQ
MLQRHYQSPQRDQLLDLTTPKPYIPTNLPPIFVPTSTNFYERALILKNSPTSRHEVSQSR
SPSASPPIKRNLYAPYDLSDRPMHSQSPKSNSPSPTPTHYDSDSSSKRIRTAFSSTQLLD
LEREFSANQYLTRLRRIEIATRLKLSEKQVKIWFQNRRVKYKKDDCPNASSEQQQQLIHA
HGSVSSGSCTNCKCSNSQPSLV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g10056.t1 | CDD | cd00086 | homeodomain | 167 | 223 | 5.5864E-21 |
| 8 | g10056.t1 | Gene3D | G3DSA:1.10.10.60 | - | 134 | 226 | 1.1E-26 |
| 12 | g10056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 110 | 129 | - |
| 15 | g10056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 110 | 126 | - |
| 14 | g10056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 141 | 167 | - |
| 13 | g10056.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 143 | 167 | - |
| 2 | g10056.t1 | PANTHER | PTHR45664:SF14 | PROTEIN ZERKNUELLT 1-RELATED | 4 | 253 | 3.0E-45 |
| 3 | g10056.t1 | PANTHER | PTHR45664 | PROTEIN ZERKNUELLT 1-RELATED | 4 | 253 | 3.0E-45 |
| 5 | g10056.t1 | PRINTS | PR00024 | Homeobox signature | 188 | 199 | 1.0E-7 |
| 6 | g10056.t1 | PRINTS | PR00024 | Homeobox signature | 203 | 213 | 1.0E-7 |
| 4 | g10056.t1 | PRINTS | PR00024 | Homeobox signature | 213 | 222 | 1.0E-7 |
| 1 | g10056.t1 | Pfam | PF00046 | Homeodomain | 167 | 223 | 1.1E-20 |
| 11 | g10056.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 199 | 222 | - |
| 16 | g10056.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 164 | 224 | 21.103 |
| 10 | g10056.t1 | SMART | SM00389 | HOX_1 | 166 | 228 | 2.5E-23 |
| 7 | g10056.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 144 | 223 | 2.31E-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 K09310 (homeobox protein GSH)
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