General information for g10817.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cohesin subunit SA-1.
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.t3 | isoform | g10817.t3 | 12136090 | 12138249 |
| chr_1 | g10817 | g10817.t3 | exon | g10817.t3.exon1 | 12136090 | 12137768 |
| chr_1 | g10817 | g10817.t3 | cds | g10817.t3.CDS1 | 12136091 | 12137768 |
| chr_1 | g10817 | g10817.t3 | exon | g10817.t3.exon2 | 12137834 | 12137898 |
| chr_1 | g10817 | g10817.t3 | cds | g10817.t3.CDS2 | 12137834 | 12137892 |
| chr_1 | g10817 | g10817.t3 | exon | g10817.t3.exon3 | 12138023 | 12138249 |
| chr_1 | g10817 | g10817.t3 | TSS | g10817.t3 | NA | NA |
| chr_1 | g10817 | g10817.t3 | TTS | g10817.t3 | NA | NA |
Sequences
>g10817.t3 Gene=g10817 Length=1971
TTATTTCGTTGATTTTAATATAAAAATTTATCAATTCAATATACCACTCGTTTGCATTTG
TTGCAATAAAAAAAAACGAAGCTATGCGACTTTATCAATCAAGTTCCAAAGAATTTTTAG
AGTGTAGAAGACTAACAACAAATAAAAATTTTTTCCTCTGCACAATTTTAAATTATTCGC
GTAAATTTAGGTGGTTTTAAATCTTTTAAATACTTTTAATTTAAAATCTTAAAATGATAA
GTCGCGGCAAAAGAATTCGTATGGATGATGTTCCAATGGAATATTCATATTATATGAATG
ACAATATTCAAGACGATGTTGATGTGGTTGAAGGTGGAACAGGTCAAAGAATGACTCGTT
TACGAGCTAGAGGTGGTGTTCCAACAAAACCACCCATTATAGATATTGATGAAGATGATG
AGGATATTTTTATGACTGGCGGTCAAAGAAAAAGAAAAATTCCGAAACCTCCAAAAGAGA
AAATTGAACGAGAACCGAGAGCACCAAGAGTTCGTAAAGAACGTGAAATTGTCGAAAAAG
AACCAGCAGAAGAACGTATTGTTAAAGAAAGAGAAATCACTACAGATGAAAACAGTTTAT
TTTGGATTTTGAGATATTCAAAGAATACAATCACTACAATTGTCGATGAATGGATTGAAA
ATTATAAAGCAGATCGTGATTCTGCTCTTATTTCACTTATGCAATTCTTCATCAATGCAA
GTGGCTGTAAAGGTAAAATCACACCAGAAATGCAAATTTCAATGGAACATACATCAATTA
TTAGAAAGATGACTGAAGAATTTGACGAAGAAAGCGGTGAATATCCTCTAATAATGGCTG
GTCAACAATGGAAGAAATTCAAAACACATTTCTGTGAATTTGTTCAAACATTGGTCAAAC
AGTGTCAGTATTCAATTATTTATGATCAATTCTTGATGGATAATATTATTTCATTACTGA
CCGGTCTTTCTGATTCGCAAGTTCGTGCTTTTCGTCATACAGCTACTCTGGCAGCAATGA
AATTGATGACGGCACTTGTCGATGTTGCTTTACTAGTGTCGATCAATCAAGACAATGCAG
CACGTCAATATGAAAGTGAAAGATTAAAAGCAGCTCATGATGTCTCTGAAGAACGTTTAG
AGAGTTTGATGGCAAAAAGACAAGAATTAGAAGAGAATATGGATGAAATTAAGAATATGT
TGACATATCTTTTTAAATCTGTGTTCGTGCACCGATATCGTGATACTTTGCCAGATATAA
GAGCCATTTGTATGATAGAAATCGGAATTTGGATGCATAAATTTTCTTCAAATTTTTTGG
ATGATTCTTATCTCAAATACATTGGGTGGACTCTTCATGATAAAGTTGGAGAAGTTCGAT
TGCGTTGTCTTCAAGCATTATTACCTCTTTATGAGAATGAAGAATTGAAAGGTAAATTGG
AATTATTTACATCTAAATTCAAAGATCGAATTGTTGCAATGACTTTGGATAAAGAATATG
AAGTTGCAGTTCATGCAGTACGTCTTGTTATAAAAATTTTAAAAATTCATCAAGACATTC
TCACAGACAAAGATTGTGAAATTGTGTATGAATTAGTTTATTCATCACATCGAGGAGTTG
CACAGGCAGCTGCGGAATTTTTAAATGTTCGACTCTTCGTTATCGACCCATCTGTCGAAT
CTTATACGAAACGAGGCAAAAAGAGATTGCCAAACACTCCACTTATTCGTGACCTCGTAC
AATTCTTCATTGAATCTGAACTTCATGAGCATGGTGCTTATTTGGTTGACTCGTTTATTG
AAAGCAATCCTATGATTAGAGATTGGGAATGTATGACAGATTTACTTCTAGAAGAGCCTG
GTCATGGAGAAGAGGCGATGGATACGAAGCAAGAATCTACTTTAATTGAGATTATGGTGA
GTGCAGTAAAGCAAGTTGCATTAGCTGAACCACCAATTGGTCGTGGAAGCA
>g10817.t3 Gene=g10817 Length=579
MISRGKRIRMDDVPMEYSYYMNDNIQDDVDVVEGGTGQRMTRLRARGGVPTKPPIIDIDE
DDEDIFMTGGQRKRKIPKPPKEKIEREPRAPRVRKEREIVEKEPAEERIVKEREITTDEN
SLFWILRYSKNTITTIVDEWIENYKADRDSALISLMQFFINASGCKGKITPEMQISMEHT
SIIRKMTEEFDEESGEYPLIMAGQQWKKFKTHFCEFVQTLVKQCQYSIIYDQFLMDNIIS
LLTGLSDSQVRAFRHTATLAAMKLMTALVDVALLVSINQDNAARQYESERLKAAHDVSEE
RLESLMAKRQELEENMDEIKNMLTYLFKSVFVHRYRDTLPDIRAICMIEIGIWMHKFSSN
FLDDSYLKYIGWTLHDKVGEVRLRCLQALLPLYENEELKGKLELFTSKFKDRIVAMTLDK
EYEVAVHAVRLVIKILKIHQDILTDKDCEIVYELVYSSHRGVAQAAAEFLNVRLFVIDPS
VESYTKRGKKRLPNTPLIRDLVQFFIESELHEHGAYLVDSFIESNPMIRDWECMTDLLLE
EPGHGEEAMDTKQESTLIEIMVSAVKQVALAEPPIGRGS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10817.t3 | Coils | Coil | Coil | 288 | 322 | - |
| 6 | g10817.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 70 | 96 | - |
| 5 | g10817.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 78 | 96 | - |
| 2 | g10817.t3 | PANTHER | PTHR11199:SF3 | COHESIN SUBUNIT SA-2 | 114 | 578 | 1.4E-205 |
| 3 | g10817.t3 | PANTHER | PTHR11199 | STROMAL ANTIGEN | 114 | 578 | 1.4E-205 |
| 1 | g10817.t3 | Pfam | PF08514 | STAG domain | 196 | 306 | 1.2E-35 |
| 8 | g10817.t3 | ProSiteProfiles | PS51425 | Stromalin conservative (SCD) domain profile. | 331 | 416 | 32.937 |
| 4 | g10817.t3 | SUPERFAMILY | SSF48371 | ARM repeat | 214 | 484 | 2.69E-16 |
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 transcript has been annotated with K06671 (cohesin complex subunit SA-1/2)
Pathway
- This transcript belongs to the following 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.
