General information for g10790.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Splicing factor 3B subunit 2.
Parent gene
- The parent gene g10790 is located on chr_1: 11995279..11996061 (- 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 | g10790 | g10790.t1 | TTS | g10790.t1 | 11993475 | 11993475 |
| chr_1 | g10790 | g10790.t1 | isoform | g10790.t1 | 11993552 | 11996061 |
| chr_1 | g10790 | g10790.t1 | exon | g10790.t1.exon1 | 11993552 | 11994144 |
| chr_1 | g10790 | g10790.t1 | cds | g10790.t1.CDS1 | 11993552 | 11994144 |
| chr_1 | g10790 | g10790.t1 | exon | g10790.t1.exon2 | 11994205 | 11994324 |
| chr_1 | g10790 | g10790.t1 | cds | g10790.t1.CDS2 | 11994205 | 11994324 |
| chr_1 | g10790 | g10790.t1 | exon | g10790.t1.exon3 | 11994398 | 11995217 |
| chr_1 | g10790 | g10790.t1 | cds | g10790.t1.CDS3 | 11994398 | 11995217 |
| chr_1 | g10790 | g10790.t1 | exon | g10790.t1.exon4 | 11995279 | 11995932 |
| chr_1 | g10790 | g10790.t1 | cds | g10790.t1.CDS4 | 11995279 | 11995932 |
| chr_1 | g10790 | g10790.t1 | exon | g10790.t1.exon5 | 11996041 | 11996061 |
| chr_1 | g10790 | g10790.t1 | cds | g10790.t1.CDS5 | 11996041 | 11996061 |
| chr_1 | g10790 | g10790.t1 | TSS | g10790.t1 | 11996152 | 11996152 |
Sequences
>g10790.t1 Gene=g10790 Length=2208
ATGGATAATAATAATCCTGAGCAAATGCATCGTTTTCCTCCTCCGCCACCAATGCTGCCA
CCACCTGGGATTCCAGCAAGTATTTCAAATAGTTGGATGAACGATGACGATTTTCCCAGA
TTTGATCAGCAAACTGCATCAAAGCCGATAATGCAACAACAACCACCGCCGCAACAAGCG
GCAAATGAAGATCCAGGAAAGAAGAAATTACCACCACCACCATTAATGTCATTGAAAATT
GACAAACCAACAAGTGGTTCAGAAAAATCTGAACTTGTTCTACCAAAAGCACTTGAAGAT
GTTTTGGCTCTTAGCTCTCAATTAAAGGAAACATCAATTCAACCTAATCAACATTCTCAA
GTTCCAGCAAATGATTTTTTGAATGACTTTGAAGCTGATGCTAGTGATGATGAAGAAAAT
AATGTACAAGCTTCAGCAAAATCTAATAAAAGTAATGATAAAAATCGTAAAAAGAAAAAG
CGTAAGAAGCAAAATCGTCAAAAAAGACAAGAGGAAGCTCAAAGAATGGCAGAGGAAAAT
CAAGAAAATCAATCTGAGACTTCGACTTCTAATGAGAAAGATAAATCAAAAGAAAAAGGT
GATGATGAGAAGGTTGACATTGAATATGTTCCTGAACGTTTGACAATTGCTGATTTAGCA
CCAATGTATAGGCAGTTTTATCGAGTTTTTGAGATATTCAAATTGGAGAATAAACCAAAA
GAAGCACCGATGCCTGTTCAAACTGCAGATGATGCAAAAGCTGCTAAAAAGGCTGCAGAA
AAAAGTGAAAGCGAAGATGAACAAGATGCTGATGAGAAAAAAGACGATAAGGATAAAATA
TCAAAACGTAAATTAAAGAAGTTGACACGACTGAGTGTTGCTGAATTAAAACAACTCGTT
AGTCGACCTGATGTAGTCGAAATGCATGATGTTACAGCGAAAGACCCTAAACTTCTTATT
CAATTGAAAGCACATCGCAATACTGTACAAGTACCTCGTCATTGGTGTTTCAAACGAAAA
TACTTGCAAGGAAAGAGAGGAATTGAAAAGCCGCCGTTTGATTTACCGGCTTTTATTAAA
AAAACTGGTATTATGGAAATGAGAGCATCTTTGCAAGAAAAAGATGAAGCGAAAACATTG
AAGGCAAAAATGCGTGAAAAGATTAGACCTAAAATGGGAAAAATTGACATTGATTATCAA
AAACTTCATGATGCATTTTTCAAATGGCAAACAAAACCAAGATTAACAATTCATGGTGAT
TTGTATTATGAAGGAAAAGAATTTGAGACTCGATTAAAAGAAAAGAAACCAGGTGATTTA
AGTGAAGAATTGCGAACAGCTCTTGGTATGCCAATTGGTCCAGCATGTCATAAAATCCCT
CCTCCTTGGTTGATTGCACAGCAACGTTATGGTCCTCCTCCAAGTTATCCAAATTTGAAG
ATTCCTGGTTTAAATGCTGCAATTCCTGATGGTTGTTGCTTTGGATATCATGCAGGTGGC
TGGGGTAAACCTCCGGTTGATAATTCAGGCAAGCCTTTATATGGCGATGTATTTGGAACA
AATAATCTTGATAACGATAGCGGTGTTGGAGATGAAGAAATTGATAGAACTTTGTGGGGA
GAACTTGAATCTGAATCAGAAGAATCATCTGAAGAAGAGGAGGAAGAAGAAGGCGATGAA
GATTTGACGGGAGCACCGGCTGATGAAAGTGGTTTAGCAACTCCAGCTGGTTTAGAGACG
CCATCTGGATTATCGAGTGTTCCTGCAGGAATGGAAACACCAGATTCAATTGAATTGCGA
AAAAAGAAAATTGAAGCCGAGATGGAAGATAATGAAACACCTGTGTTATATCACGTGTTG
CCTGAAAAGAGAAATGAGAGAATTGGTGGTTCAATGATGGCATCAACTCATGTTTACGAT
GTTTCTGGTGGAGCAGCTTTAGCTCAATCAGCTGCACGTAGAACGACCCATGTCGAACGA
GAAGGCATGGTTGAATTAGCTTTGAATCCTGATGAACTTGATTTAGATAATGAAGCAATG
GCTCAAAGATATGAGCAACAAATGAGAGAACAACAAAGTCATTTGCAAAAGGAAGATTTA
TCTGATATGTTGGCAGAACATGTTGCACGTCAAAAGTCAAAACGCAAAAGACAGCAAACA
ACAACTAATCCTAAGCAAAAAGAAGACTACAAAAAGTTTAAATTCTGA
>g10790.t1 Gene=g10790 Length=735
MDNNNPEQMHRFPPPPPMLPPPGIPASISNSWMNDDDFPRFDQQTASKPIMQQQPPPQQA
ANEDPGKKKLPPPPLMSLKIDKPTSGSEKSELVLPKALEDVLALSSQLKETSIQPNQHSQ
VPANDFLNDFEADASDDEENNVQASAKSNKSNDKNRKKKKRKKQNRQKRQEEAQRMAEEN
QENQSETSTSNEKDKSKEKGDDEKVDIEYVPERLTIADLAPMYRQFYRVFEIFKLENKPK
EAPMPVQTADDAKAAKKAAEKSESEDEQDADEKKDDKDKISKRKLKKLTRLSVAELKQLV
SRPDVVEMHDVTAKDPKLLIQLKAHRNTVQVPRHWCFKRKYLQGKRGIEKPPFDLPAFIK
KTGIMEMRASLQEKDEAKTLKAKMREKIRPKMGKIDIDYQKLHDAFFKWQTKPRLTIHGD
LYYEGKEFETRLKEKKPGDLSEELRTALGMPIGPACHKIPPPWLIAQQRYGPPPSYPNLK
IPGLNAAIPDGCCFGYHAGGWGKPPVDNSGKPLYGDVFGTNNLDNDSGVGDEEIDRTLWG
ELESESEESSEEEEEEEGDEDLTGAPADESGLATPAGLETPSGLSSVPAGMETPDSIELR
KKKIEAEMEDNETPVLYHVLPEKRNERIGGSMMASTHVYDVSGGAALAQSAARRTTHVER
EGMVELALNPDELDLDNEAMAQRYEQQMREQQSHLQKEDLSDMLAEHVARQKSKRKRQQT
TTNPKQKEDYKKFKF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g10790.t1 | Coils | Coil | Coil | 154 | 186 | - |
| 21 | g10790.t1 | Coils | Coil | Coil | 367 | 387 | - |
| 18 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 92 | - |
| 16 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 9 | 24 | - |
| 13 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 27 | 60 | - |
| 7 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 124 | - |
| 14 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 109 | 210 | - |
| 19 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 152 | 166 | - |
| 6 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 188 | 210 | - |
| 15 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 241 | 279 | - |
| 12 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 253 | 279 | - |
| 8 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 565 | - |
| 9 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 544 | 564 | - |
| 10 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 682 | 735 | - |
| 17 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 690 | 709 | - |
| 11 | g10790.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 721 | 735 | - |
| 3 | g10790.t1 | PANTHER | PTHR12785:SF6 | SPLICING FACTOR 3B SUBUNIT 2 | 135 | 735 | 9.2E-228 |
| 4 | g10790.t1 | PANTHER | PTHR12785 | SPLICING FACTOR 3B | 135 | 735 | 9.2E-228 |
| 2 | g10790.t1 | Pfam | PF04037 | Domain of unknown function (DUF382) | 302 | 427 | 3.5E-57 |
| 1 | g10790.t1 | Pfam | PF04046 | PSP | 436 | 486 | 1.1E-18 |
| 5 | g10790.t1 | SMART | SM00581 | testneu | 432 | 490 | 5.9E-28 |
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:0005634 | nucleus | CC |
KEGG
Orthology
- This transcript has been annotated with K12829 (splicing factor 3B subunit 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.
