General information for g10817.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cohesin subunit SA-2.
Parent gene
- The parent gene g10817 is located on chr_1: 12136690..12138249 (- 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 | g10817 | g10817.t4 | isoform | g10817.t4 | 12136690 | 12137768 |
| chr_1 | g10817 | g10817.t4 | exon | g10817.t4.exon1 | 12136690 | 12137768 |
| chr_1 | g10817 | g10817.t4 | cds | g10817.t4.CDS1 | 12136691 | 12137767 |
| chr_1 | g10817 | g10817.t4 | TSS | g10817.t4 | 12138128 | 12138128 |
| chr_1 | g10817 | g10817.t4 | TTS | g10817.t4 | NA | NA |
Sequences
>g10817.t4 Gene=g10817 Length=1079
TATGAATGACAATATTCAAGACGATGTTGATGTGGTTGAAGGTGGAACAGGTCAAAGAAT
GACTCGTTTACGAGCTAGAGGTGGTGTTCCAACAAAACCACCCATTATAGATATTGATGA
AGATGATGAGGATATTTTTATGACTGGCGGTCAAAGAAAAAGAAAAATTCCGAAACCTCC
AAAAGAGAAAATTGAACGAGAACCGAGAGCACCAAGAGTTCGTAAAGAACGTGAAATTGT
CGAAAAAGAACCAGCAGAAGAACGTATTGTTAAAGAAAGAGAAATCACTACAGATGAAAA
CAGTTTATTTTGGATTTTGAGATATTCAAAGAATACAATCACTACAATTGTCGATGAATG
GATTGAAAATTATAAAGCAGATCGTGATTCTGCTCTTATTTCACTTATGCAATTCTTCAT
CAATGCAAGTGGCTGTAAAGGTAAAATCACACCAGAAATGCAAATTTCAATGGAACATAC
ATCAATTATTAGAAAGATGACTGAAGAATTTGACGAAGAAAGCGGTGAATATCCTCTAAT
AATGGCTGGTCAACAATGGAAGAAATTCAAAACACATTTCTGTGAATTTGTTCAAACATT
GGTCAAACAGTGTCAGTATTCAATTATTTATGATCAATTCTTGATGGATAATATTATTTC
ATTACTGACCGGTCTTTCTGATTCGCAAGTTCGTGCTTTTCGTCATACAGCTACTCTGGC
AGCAATGAAATTGATGACGGCACTTGTCGATGTTGCTTTACTAGTGTCGATCAATCAAGA
CAATGCAGCACGTCAATATGAAAGTGAAAGATTAAAAGCAGCTCATGATGTCTCTGAAGA
ACGTTTAGAGAGTTTGATGGCAAAAAGACAAGAATTAGAAGAGAATATGGATGAAATTAA
GAATATGTTGACATATCTTTTTAAATCTGTGTTCGTGCACCGATATCGTGATACTTTGCC
AGATATAAGAGCCATTTGTATGATAGAAATCGGAATTTGGATGCATAAATTTTCTTCAAA
TTTTTTGGATGATTCTTATCTCAAATACATTGGGTGGACTCTTCATGATAAAGTTGGAG
>g10817.t4 Gene=g10817 Length=359
MNDNIQDDVDVVEGGTGQRMTRLRARGGVPTKPPIIDIDEDDEDIFMTGGQRKRKIPKPP
KEKIEREPRAPRVRKEREIVEKEPAEERIVKEREITTDENSLFWILRYSKNTITTIVDEW
IENYKADRDSALISLMQFFINASGCKGKITPEMQISMEHTSIIRKMTEEFDEESGEYPLI
MAGQQWKKFKTHFCEFVQTLVKQCQYSIIYDQFLMDNIISLLTGLSDSQVRAFRHTATLA
AMKLMTALVDVALLVSINQDNAARQYESERLKAAHDVSEERLESLMAKRQELEENMDEIK
NMLTYLFKSVFVHRYRDTLPDIRAICMIEIGIWMHKFSSNFLDDSYLKYIGWTLHDKVG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10817.t4 | Coils | Coil | Coil | 268 | 302 | - |
| 5 | g10817.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 39 | 76 | - |
| 6 | g10817.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 58 | 76 | - |
| 2 | g10817.t4 | PANTHER | PTHR11199:SF3 | COHESIN SUBUNIT SA-2 | 94 | 359 | 7.7E-123 |
| 3 | g10817.t4 | PANTHER | PTHR11199 | STROMAL ANTIGEN | 94 | 359 | 7.7E-123 |
| 1 | g10817.t4 | Pfam | PF08514 | STAG domain | 176 | 286 | 5.1E-36 |
| 8 | g10817.t4 | ProSiteProfiles | PS51425 | Stromalin conservative (SCD) domain profile. | 311 | 359 | 23.045 |
| 4 | g10817.t4 | SUPERFAMILY | SSF48371 | ARM repeat | 188 | 356 | 1.5E-5 |
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.
