General information for g12247.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Structural maintenance of chromosomes protein 3.
Parent gene
- The parent gene g12247 is located on chr_1: 21983552..21987095 (+ 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 | g12247 | g12247.t2 | TSS | g12247.t2 | 21983136 | 21983136 |
| chr_1 | g12247 | g12247.t2 | isoform | g12247.t2 | 21983276 | 21984384 |
| chr_1 | g12247 | g12247.t2 | exon | g12247.t2.exon1 | 21983276 | 21983290 |
| chr_1 | g12247 | g12247.t2 | exon | g12247.t2.exon2 | 21983387 | 21984384 |
| chr_1 | g12247 | g12247.t2 | cds | g12247.t2.CDS1 | 21983810 | 21984382 |
| chr_1 | g12247 | g12247.t2 | TTS | g12247.t2 | 21984384 | 21984384 |
Sequences
>g12247.t2 Gene=g12247 Length=1013
ATGCATATTAAACAGGTCATTATTCACGGTTTCAAGTCATATCGCGAACAAACTGTCGTC
GATCCGTTCCATAAAAAGCATAATGTAGTCGTCGGAAGAAATGGTAGTGGCAAGAGCAAT
TTTTTCTCAGCAATTCAATTTGTTCTTAGTGATGAATTTACACATCTACGCCCAGAACAG
CGTTAGAATCTTTTACATGAAGGTGTTGGTCAACGATTGGGTTCGGCCTATGTAGAAATT
ATATTTGACAATTCTGATAATCGTGTTCCAATTGATAAAGAAGAAATTTCTTTAAAGCGA
GTTATTGGTGCAAAAAAAGATCAATATTTCCTCAACAAAAAGAATGTTCCAAGATCAGAA
GTTGTCAATTTGCTTGAATCAGCAGGTTTTTCAAATTCAAATCCTTATTACATTGTAAAA
CAAGGTAAAATCAATCAAATGGCCACAGCTCCAGATGCACATCGATTGAAATTATTAAGA
GAAGTTGCTGGTACAAGAGTATATGATGAACGCAAAGAAGAATCCAAGACAATTTTGAAA
GATACAGATTCAAAAGTGGAAAAAATTACAGAATTTTTAAAAACTATCGAAGAACGTTTA
AAAACTCTTGAAGAAGAAAAGGAAGAATTGAAAGAATATCAAAAATGGGACAAGCTTCGA
AGAATGCTTGAATATATAATTTACGAGACAGAGTTAAAAGAGAATCGTAAACAGCTTGAT
GATCTTGAAAATCATCGTAAAAATTCAGGAGATCAGCAAAAGAAACTAACAAATGAGATT
CAAAAAATACAAGATAAAATCAAAAACATACAGAAGAATCTCAAAGATGCTAAGAAAGAA
GTGACTACTTGTAAAGAAGAACGATCTGTATTAGTTGCTGAACAACAGCAATTGTTGCGT
GAGAAAACTAAATTGGATCTAACAATTAATGATTTGAATGATGAAGTTCAAGGTGACAAT
AAGTCAAAAGAAAGAGCAGAACAAGAATTGAAACGACTCGAAATAACTATTGC
>g12247.t2 Gene=g12247 Length=191
MATAPDAHRLKLLREVAGTRVYDERKEESKTILKDTDSKVEKITEFLKTIEERLKTLEEE
KEELKEYQKWDKLRRMLEYIIYETELKENRKQLDDLENHRKNSGDQQKKLTNEIQKIQDK
IKNIQKNLKDAKKEVTTCKEERSVLVAEQQQLLREKTKLDLTINDLNDEVQGDNKSKERA
EQELKRLEITI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12247.t2 | Coils | Coil | Coil | 40 | 67 | - |
| 6 | g12247.t2 | Coils | Coil | Coil | 79 | 141 | - |
| 4 | g12247.t2 | Coils | Coil | Coil | 149 | 190 | - |
| 3 | g12247.t2 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 103 | 1.1E-5 |
| 1 | g12247.t2 | PANTHER | PTHR43977 | STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 | 1 | 188 | 3.2E-51 |
| 2 | g12247.t2 | PANTHER | PTHR43977:SF1 | STRUCTURAL MAINTENANCE OF CHROMOSOMES PROTEIN 3 | 1 | 188 | 3.2E-51 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
