Gene loci information

Transcript annotation

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

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 g10306 g10306.t1 TTS g10306.t1 8868381 8868381
chr_1 g10306 g10306.t1 isoform g10306.t1 8868464 8873421
chr_1 g10306 g10306.t1 exon g10306.t1.exon1 8868464 8868474
chr_1 g10306 g10306.t1 cds g10306.t1.CDS1 8868464 8868474
chr_1 g10306 g10306.t1 exon g10306.t1.exon2 8868660 8868696
chr_1 g10306 g10306.t1 cds g10306.t1.CDS2 8868660 8868696
chr_1 g10306 g10306.t1 exon g10306.t1.exon3 8868894 8868970
chr_1 g10306 g10306.t1 cds g10306.t1.CDS3 8868894 8868970
chr_1 g10306 g10306.t1 exon g10306.t1.exon4 8869038 8870868
chr_1 g10306 g10306.t1 cds g10306.t1.CDS4 8869038 8870868
chr_1 g10306 g10306.t1 exon g10306.t1.exon5 8871059 8871366
chr_1 g10306 g10306.t1 cds g10306.t1.CDS5 8871059 8871366
chr_1 g10306 g10306.t1 exon g10306.t1.exon6 8871788 8872963
chr_1 g10306 g10306.t1 cds g10306.t1.CDS6 8871788 8872963
chr_1 g10306 g10306.t1 exon g10306.t1.exon7 8873196 8873421
chr_1 g10306 g10306.t1 cds g10306.t1.CDS7 8873196 8873421
chr_1 g10306 g10306.t1 TSS g10306.t1 8873950 8873950

Sequences

>g10306.t1 Gene=g10306 Length=3666
ATGTACCTATATAATCTAACACTTCAGCGTGCGACTGGCATTACATGTGCCATTCATGGA
AATTTTTCGGGTTCAAAATTACAAGAAATATTAATATCACATGGCAAAAGTTTGGAATTA
CTAAGGCCTGATCCGAATACCGGCAAAGTCCATACACTTTTGCAAACTGAAATATTTGGT
GTAATTCGTTCTATGATGGCTTTTCGATTAACTGGATCAACAAAAGATTATGCCATTATT
GGATCAGATTCAGGAAGAATTTTAATTTTGGAGTATAATCAAGCTAAAAATCAGCTCGTA
AAAGTACAATTAGAAACATTTGGCAAATCAGGATGTCGAAGAATAGTACCGGGTCAATAT
TTAGCTGTAGATCCCAAAGGACGAGCTGTAATGATTGGAGCAATCGAAAAACAAAAGTTG
GTTTACATTCTTAATCGTGATTCTGAAAATCATTTAACAATCTCATCTCCACTAGAAGCA
CACAAATCTAACACACTTTGCTATCATATGGTTGGAGTTGATAATGGTTTTGATAATCCA
ATGTTTGCCTGCTTAGAAATTGATTATGGTGAAATAGACTGTGATCCTTCAGGTGAAGCA
GCTGCAAGAGCTAAACAAATCATTACATTTTATGAACTCGATTTGGGTTTGAATCATGTT
GTACGAAAATATCACGAAGAACTCGATGAGCACGCAAATTTCTTGATCACTGTTCCTGGT
GGCGGTGATGGCCCTTCTGGTGTTTTAATTTGTTCAGAAAACTATGTGACTTATAAAAAC
ACCGGAGCACAAGCAGATATTCGTTGTCCAATTCCTCGACGAAGAAATGATCTCGATGAT
CCTGAGCGTGGAATGATTTTTATTTGCTCTGCTACTCATAAAACAAAATCAATGTTTTTC
TTCTTACTACAAACTGAACAAGGAGATATTTTTAAAGTCACTCTCGATATGAATGAAGAT
GCTGTTTCTGCCATCAAATTAAAGTATTTCGATACAGTACCTCCAGCTACGACACTTTCC
GTTTTAAAATCTGGATTTTTATTTGTGGCTTGTGAATTTGGTAATCATTATCTCTATCAA
ATTGCTCATCTTGGTGACGATGAAGAGGAACCAGAATTTAGTAGCGCAATGCCTTTAGAA
GAGGGTGATACATTTTTCTTCGCTCCTCGACCGCTCAAAAATCTTGTTATGGTCGATGAA
ATTCCTTCTTATGCACCAATAATGTCAAGTCATGTAGCTGATTTAGCAAACGAAGATACA
CCACAATTATATTTGGCATGTGGAAGAGGACCACGATCATCAATTCGTGTTTTAAGGCAT
GGATTAGAAGTATCTGAAATGGCTGTCTCAGAACTTCCTGGTATCCCGCTTTCAGTTTGG
TCAATCAAGAAACGTGTTGATGATGAATTTGATGCATACATCATTGTATCTTTCGTAAAT
GCTACCTTGGTATTGAGCATTGGTGACACTGTTGAGGAAGTAACAGATAGTGGATTTTTA
GGAACTACTCCTACACTTTGCTGCGCTTCACTTGGAGATGATGCTTTGGTTCAGATTTAT
CCTGATGGTATTAGACACATTCGAGCTGATCGAAGAGTAAACGAATGGAAAGCACCAAAT
AAAAAGACAATTGTGAAATGTGCAGTTAATCAGCGTCAAGTTGTAATTGCTTTATCTGGT
GGTGATCTCGTTTATTTTGAAATGGATCCGACTGGTCAATTAAATGAGTTTACTGAACGA
AGAAAAATGATGGCTGATATATTGTGTATGACATTAGCTTCAATAAAACCTGGTGAACTA
CAATCTCCGTTTTTAGCAGTTGGTTTAGCTGACAGCACAGTTCGAGTCATATCACTACAG
AGACAAGATTGTCTTCAACCACGCTCAATGCAAGCTTTACCATCGCCAGCAGAATCATTA
TGTTTGGTAGAAATGGGAATTGGTGAGACTGAAGAAGATGAAGATGGTGTCATTATTCAT
AAAGGAGGAAAAGAAAAAGGATCATTATATCTCAACATAGGTCTGCAAAATGGTGTTTTA
TTGCGAACAGTATTGGATAAGATATCGGGTGATTTGACTGATACACGAACACGTTATTTA
GGATCGCGTGGTGTAAAGCTTTTTAGAATTAAAGTACAAGGAAGTGAAGCTGTTCTGGCA
ATGTCTTCAAGATCGTGGCTCAGTTATTATTATCAAAATCGTTTTCATTTAACACCATTA
AGTTATGAGACACTCGAATATGCATCAGGATTCTCATCAGAGCAGTGTTCAGAAGGTATT
GTTGCAATTTCAACGAATACATTACGAATTTTGGCATTGGAAAAACTAGGAGCTGTTTTC
AATCAAATTTCATTTCCTCTCGAGTATACGCCCAAAAGATTCGTTGTTCATACTGATACT
TCACGATTAATTGTTGCTGAAACAGATCATAATGCATACACTGAGGCAACGAAAAATCTC
AGAAAACGTCAAATGGCTGATGAAATGATTGAAGCTGCAGGCGAGAATGAACAAGAATTA
GCACAAGAGCTTGCTGATGCTTTTATTAATGAAGTTTTACCCGAAGATACATTTTCAGCA
CCAAAAGCAGGCTATGGAATGTGGGCATCACAAATTAGAATTATGGATCCTGTCAAAGGT
CAGACGTTATTCAAAGTACCACTTGAACAGAATGAAGCAGTTGTATCAATGTGTTTAGTT
AAATTCAGCGTTGATGGTAAAAGTTATTTAGCATGCGGTGTTGTTAAAGACATGCAGTTA
AATCCACGACAAATTGGTTCTGGCTATATCGATTTATATCGAGTCGATAATCAATGTGCA
ACGCTGAATTTGATTCATAGAACAGAAGTTGAAGATATTCCATCAGCAATAGCACCTTTT
CAAGGTAAACTATTAGTTGGAGTTGGAAAGATTTTGCGAGTTTATGATTTAGGCAAGAAA
AAGTTATTAAGAAAATGCGAAAATAAGCACATCCCTAATCAAATTGTCAATATTCAAACG
AGAGCTTTACGTGTATTTTGCTCAGATGTACAAGAAAGTGTTTATTGTCTCACATACAAG
CGAAATGAAAATCAATTGATTATTTTTGCTGATGACACTTTCCCTCGATGGATAACAACA
ACAGCAATTTTGGATTATGATACAATAGCTACAGGTGACAAGTTTGGAAATATTGCCATT
TTGAGACTACCGCATTCTATCAATGATGATGTGGACGAAGATCCAACGGGAAACAAAGCA
CTTTGGGATCGAGGTTTGCTAAATGGAGCATCACAAAAAGCTGAAAACATAATCACATTC
CATATTGGTGAGATAGTAATGTCGCTACAAAAATCAATGTTGATTCCTGGTGGTCCAGAA
CTTTTAATTTATACAACAATTAGCGGTACAATTGGTGCATTAGTTCCATTTACAGGAAGA
GAAGATTTTGATTTCTTTCAACATTTAGAAATGCACATGAGAAATGAAAATCCACCATTG
TGTGGTAGAGATCATTTGAGTTATAGATCTTACTATTATCCAGTAAAGAATGTCATTGAT
GTCGAAGTGCAACTGAGGTGGCAAAGAAGCTTGAAGATATTAGAACAAGATACGCATTTT
AAATTTTTTCACAGTCAAATTGTAATTTTAAAAAGTGACGGTAGTGAAAATGAATGTTTT
CTTTAA

>g10306.t1 Gene=g10306 Length=1221
MYLYNLTLQRATGITCAIHGNFSGSKLQEILISHGKSLELLRPDPNTGKVHTLLQTEIFG
VIRSMMAFRLTGSTKDYAIIGSDSGRILILEYNQAKNQLVKVQLETFGKSGCRRIVPGQY
LAVDPKGRAVMIGAIEKQKLVYILNRDSENHLTISSPLEAHKSNTLCYHMVGVDNGFDNP
MFACLEIDYGEIDCDPSGEAAARAKQIITFYELDLGLNHVVRKYHEELDEHANFLITVPG
GGDGPSGVLICSENYVTYKNTGAQADIRCPIPRRRNDLDDPERGMIFICSATHKTKSMFF
FLLQTEQGDIFKVTLDMNEDAVSAIKLKYFDTVPPATTLSVLKSGFLFVACEFGNHYLYQ
IAHLGDDEEEPEFSSAMPLEEGDTFFFAPRPLKNLVMVDEIPSYAPIMSSHVADLANEDT
PQLYLACGRGPRSSIRVLRHGLEVSEMAVSELPGIPLSVWSIKKRVDDEFDAYIIVSFVN
ATLVLSIGDTVEEVTDSGFLGTTPTLCCASLGDDALVQIYPDGIRHIRADRRVNEWKAPN
KKTIVKCAVNQRQVVIALSGGDLVYFEMDPTGQLNEFTERRKMMADILCMTLASIKPGEL
QSPFLAVGLADSTVRVISLQRQDCLQPRSMQALPSPAESLCLVEMGIGETEEDEDGVIIH
KGGKEKGSLYLNIGLQNGVLLRTVLDKISGDLTDTRTRYLGSRGVKLFRIKVQGSEAVLA
MSSRSWLSYYYQNRFHLTPLSYETLEYASGFSSEQCSEGIVAISTNTLRILALEKLGAVF
NQISFPLEYTPKRFVVHTDTSRLIVAETDHNAYTEATKNLRKRQMADEMIEAAGENEQEL
AQELADAFINEVLPEDTFSAPKAGYGMWASQIRIMDPVKGQTLFKVPLEQNEAVVSMCLV
KFSVDGKSYLACGVVKDMQLNPRQIGSGYIDLYRVDNQCATLNLIHRTEVEDIPSAIAPF
QGKLLVGVGKILRVYDLGKKKLLRKCENKHIPNQIVNIQTRALRVFCSDVQESVYCLTYK
RNENQLIIFADDTFPRWITTTAILDYDTIATGDKFGNIAILRLPHSINDDVDEDPTGNKA
LWDRGLLNGASQKAENIITFHIGEIVMSLQKSMLIPGGPELLIYTTISGTIGALVPFTGR
EDFDFFQHLEMHMRNENPPLCGRDHLSYRSYYYPVKNVIDVEVQLRWQRSLKILEQDTHF
KFFHSQIVILKSDGSENECFL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g10306.t1 Gene3D G3DSA:2.130.10.10 - 4 1070 0e+00
8 g10306.t1 Gene3D G3DSA:2.130.10.10 - 13 403 0e+00
7 g10306.t1 Gene3D G3DSA:2.130.10.10 - 442 778 0e+00
3 g10306.t1 PANTHER PTHR10644 DNA REPAIR/RNA PROCESSING CPSF FAMILY 2 1181 0e+00
4 g10306.t1 PANTHER PTHR10644:SF1 SPLICING FACTOR 3B SUBUNIT 3 2 1181 0e+00
1 g10306.t1 Pfam PF10433 Mono-functional DNA-alkylating methyl methanesulfonate N-term 76 592 0e+00
2 g10306.t1 Pfam PF03178 CPSF A subunit region 869 1184 0e+00
5 g10306.t1 SUPERFAMILY SSF50978 WD40 repeat-like 550 1067 1e-07

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
GO:0005515 protein binding MF
GO:0003676 nucleic acid binding MF

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