Gene loci information

Transcript annotation

  • This transcript has been annotated as Splicing factor 3B subunit 1.

Parent gene

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 g12167 g12167.t1 TTS g12167.t1 21437529 21437529
chr_1 g12167 g12167.t1 isoform g12167.t1 21438330 21441110
chr_1 g12167 g12167.t1 exon g12167.t1.exon1 21438330 21441110
chr_1 g12167 g12167.t1 cds g12167.t1.CDS1 21438330 21441110
chr_1 g12167 g12167.t1 TSS g12167.t1 NA NA

Sequences

>g12167.t1 Gene=g12167 Length=2781
ATGTCAATGGCAACACTAACTCCTGGTCATTTGGCTTCAATGACACCTGAACAATTGCAA
GATGAAGAATTGGACTCATTATTCCCACCTGGTTATAAAATTCTTCCCGCTCCTGCTGGC
TATATTCCTATTAGAACTGCAGCCAGAAAATTAACTGCAACACCTACACCAATAGCAGGA
ACTCCGACAGGATTTTTCATTCAACAAGAAGACAAAACAGCTGCAAAATTTAATGATAAT
CAACCAAAAGGAAATTTACCGTTTATGAAACCAGAAGATGCTCAATATTTTGATAAATTG
CTTGTTGATGTCGATGAAGAAGCTCTAAGTCCAGAAGAACAGCGTGAAAGAAAAATTATG
AAATTGCTATTAAAAATTAAAAATGGAACTCCACCAATGAGAAAAGCTGCATTGCGTCAA
ATTACCGATAAAGCAAGAGAATTCGGAGCTGGACCATTGTTTAATCAAATTTTACCATTG
CTTATGTCACCAACACTTGAAGATCAAGAACGTCATTTACTTGTTAAAGTTATTGATCGA
ATTCTTTATAAATTGGATGATTTGGTACGACCATATGTGCACAAAATTCTTGTCGTTATT
GAACCGCTATTGATTGATGAAGATTACTATGCACGTGTTGAAGGTCGTGAAATCATATCG
AATTTAGCAAAAGCAGCTGGTCTCGCAACAATGATCAGTACTATGCGTCCTGATATCGAT
AACATTGATGAATATGTAAGAAATACAACAGCAAGAGCTTTCGCAGTTGTCGCTTCATCA
CTTGGAATTCCATCACTTTTGCCATTCTTGAAAGCTGTCTGTAAAAGTAAGAAATCATGG
CAAGCACGTCACACTGGTATAAAAATTGTGCAACAAATTGCAATTCTTATGGGATGCGCT
ATTTTGCCTCATTTAAAATCATTGGTTGAAATTATTGAGCATGGTTTAGTAGATGAACAA
CAAAAAGTCAGAACAATTACTGCTCTCGCATTAGCTGCTTTAGCAGAAGCTTCGACTCCT
TACGGTATTGAAAGTTTCGATTCAGTTTTGAAACCATTATGGAAAGGTATTCGAACTCAT
CGTGGAAAGGGCTTAGCTGCATTTTTGAAAGCTATTGGTTATTTAATTCCATTGATGGAT
GCTGAATATGCAAATTATTACACACGTGAAGTAATGTTGATTTTAATTCGTGAATTTCAA
TCGCCAGATGAAGAAATGAAGAAGATTGTATTGAAAGTTGTAAAGCAATGTTGTGCAACG
GATGGTGTTGAGGCACAATACATTAAAGAAGAAATTTTGCCGCATTTCTTTAAACATTTT
TGGAATCATCGTATGGCATTGGATCGACGCAATTATCGTCAATTGGTCGATACAACTGTA
GAAATTGCAAATAAAGTTGGCTCATCGGAAATCATTAATCGCGTTGTAGATGATTTAAAA
GATGAAAATGAACAATATCGCAAAATGGTAATGGAGACTGTTGAGAAAATTATGGGAAAT
CTTGGCGCTGCAGATATCGATTCTCGTTTAGAAGAGCAGCTTATTGATGGTATTTTATAT
GCGTTCCAAGAGCAAACAACTGAAGATGTTGTTATGTTAAATGGATTTGGTACAATTGTA
AACCAATTAAGCAAAAGAGTTAAACCGTATTTGCCACAAATTTGCGGTACAATTTTATGG
CGTTTAAATAACAAATCAGCAAAAGTTAGACAGCAAGCAGCAGATTTGATTTCAAGAATT
GCTGTCGTTATGAAAACATGTCAAGAAGAGAAACTCATGGGACATTTGGGTGTTGTTTTA
TATGAATATCTTGGTGAAGAATATCCAGAAGTTCTTGGTTCAATTTTGGGCGCATTGAAA
GCTATTGTAAATGTGATTGGTATGACAAAAATGACTCCACCAATTAAAGATTTGTTGCCT
CGTTTGACTCCAATTTTAAAGAATCGTCATGAGAAAGTACAAGAAAATTGTATTGATTTG
GTTGGACGAATTGCTGACCGTGGCCCTGAATATGTTTCAGCTCGTGAATGGATGAGAATT
TGCTTTGAATTATTAGAATTGCTAAAAGCTCACAAGAAGGCAATTCGTAGAGCAACTGTC
AACACATTTGGTTATATTGCAAAAGCTATTGGTCCTCATGATGTGCTCGCTACATTGCTC
AATAATTTGAAAGTTCAAGAACGTCAAAATCGTGTTTGTACAACTGTCGCTATTGCTATT
GTAGCTGAAACATGCAGACCATTCACAGTCTTACCTGCATTAATGAATGAATATCGAGTA
CCAGAATTGAATGTACAAAATGGTGTTTTAAAGTCATTGTCATTCCTGTTTGAATATATC
GGTGAGATGGGCAAGGATTATATTTATGCTGTCGTTCCATTACTTGAAGATGCTTTGATG
GATCGTGATTTAGTACACAGACAAACAGCATGTGCAGCAATTAAACATATGTCGCTTGGT
GTTTATGGCTTTGGCTGCGAAGATGCACTTGTGCATTTATTAAATTATGTTTGGCCAAAT
ATTTTTGAAACCTCACCTCATCTTGTTCAAGCATTCATGGATGCTGTCGAAGGACTTCGA
GTAGCGCTTGGACCAATTAAAATTTTACAGTACACATTACAAGGTTTATTTCATCCAGCA
AGAAAAGTTCGTGACGTCTATTGGAAAATTTATAATTCACTTTATATCGGAGCACAAGAT
GCACTAATAGCAGGCTTTCCACGCATCGAAAATGATCCTAAAAACCAATATATTCGCTAC
GAACTTGATTATAATTTATAA

>g12167.t1 Gene=g12167 Length=926
MSMATLTPGHLASMTPEQLQDEELDSLFPPGYKILPAPAGYIPIRTAARKLTATPTPIAG
TPTGFFIQQEDKTAAKFNDNQPKGNLPFMKPEDAQYFDKLLVDVDEEALSPEEQRERKIM
KLLLKIKNGTPPMRKAALRQITDKAREFGAGPLFNQILPLLMSPTLEDQERHLLVKVIDR
ILYKLDDLVRPYVHKILVVIEPLLIDEDYYARVEGREIISNLAKAAGLATMISTMRPDID
NIDEYVRNTTARAFAVVASSLGIPSLLPFLKAVCKSKKSWQARHTGIKIVQQIAILMGCA
ILPHLKSLVEIIEHGLVDEQQKVRTITALALAALAEASTPYGIESFDSVLKPLWKGIRTH
RGKGLAAFLKAIGYLIPLMDAEYANYYTREVMLILIREFQSPDEEMKKIVLKVVKQCCAT
DGVEAQYIKEEILPHFFKHFWNHRMALDRRNYRQLVDTTVEIANKVGSSEIINRVVDDLK
DENEQYRKMVMETVEKIMGNLGAADIDSRLEEQLIDGILYAFQEQTTEDVVMLNGFGTIV
NQLSKRVKPYLPQICGTILWRLNNKSAKVRQQAADLISRIAVVMKTCQEEKLMGHLGVVL
YEYLGEEYPEVLGSILGALKAIVNVIGMTKMTPPIKDLLPRLTPILKNRHEKVQENCIDL
VGRIADRGPEYVSAREWMRICFELLELLKAHKKAIRRATVNTFGYIAKAIGPHDVLATLL
NNLKVQERQNRVCTTVAIAIVAETCRPFTVLPALMNEYRVPELNVQNGVLKSLSFLFEYI
GEMGKDYIYAVVPLLEDALMDRDLVHRQTACAAIKHMSLGVYGFGCEDALVHLLNYVWPN
IFETSPHLVQAFMDAVEGLRVALGPIKILQYTLQGLFHPARKVRDVYWKIYNSLYIGAQD
ALIAGFPRIENDPKNQYIRYELDYNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12167.t1 Coils Coil Coil 476 496 -
7 g12167.t1 Gene3D G3DSA:1.25.10.10 - 101 345 4.4E-9
6 g12167.t1 Gene3D G3DSA:1.25.10.10 - 375 820 1.8E-24
2 g12167.t1 PANTHER PTHR12097 SPLICING FACTOR 3B, SUBUNIT 1-RELATED 18 922 0.0
3 g12167.t1 PANTHER PTHR12097:SF1 BNAA06G23400D PROTEIN 18 922 0.0
1 g12167.t1 Pfam PF08920 Splicing factor 3B subunit 1 19 72 2.2E-19
5 g12167.t1 SMART SM01349 TOG_3 498 738 0.0044
4 g12167.t1 SUPERFAMILY SSF48371 ARM repeat 122 920 4.48E-102

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:0003729 mRNA binding MF
GO:0000245 spliceosomal complex assembly BP

KEGG

Orthology

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.

Raw TPM values