Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Splicing factor 45.

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_2 g6229 g6229.t2 TSS g6229.t2 15424518 15424518
chr_2 g6229 g6229.t2 isoform g6229.t2 15424787 15425763
chr_2 g6229 g6229.t2 exon g6229.t2.exon1 15424787 15425763
chr_2 g6229 g6229.t2 cds g6229.t2.CDS1 15425227 15425763
chr_2 g6229 g6229.t2 TTS g6229.t2 15425785 15425785

Sequences

>g6229.t2 Gene=g6229 Length=977
CAGTTGCAAGCTTGAAACCGAAAGTAATTGATGAAAATAAACCTAAAGAAGTCATTGTGA
AGCCGAAAATCATTCAAAGTCAACCACTTCAGCCTGTAGTTGTTCAACCTAAAATAATAA
GCCATACAAATAATGAATGGGATGATTTCTTATCAATTCAAGATGAATATAATCCTGCAA
TTCCAAATGAATATGAGAAAATTGTAAAAGAAAGGCGAGAAAGAAACAAAAAGGATGATC
GAAAAAGACATCGATCACCATCGCCAAGAAAAAGTTTCAACAGACGAAATTCAGATGATG
AAGATTTCAGACCGACACTTGGTGGTTCTCGAAACAGTGGAACAGCAATTGCTCCACCAA
AATCATTACAAGAAAGCTCTCCAATTATCGATATTCCAAACATTACTCAGTATGGAGCAT
CAACTATTGCTGGAAGAATTATGGCAAAATACGGTTTTAAAGATGGACAAGGATTAGGCA
AGCAAGAACAAGGAATTAGCAGTGCATTACAAGTTGAAAAAACTTCAAAACGCGGGGGTC
GAATAATTAGTGAAAAAGAAGTCAAAGAGATGTCAACAATAACACAAACTCCACAACAGC
AACAAGCACAACCAGAGCCACAAACTTCTCAAAATCCTTCTCTACCAAGTGAACAGAGCA
TCACAGAAATGATGAAGAATCCAAGCAAAGTAATTTTACTCAGAAATATGGTTGGTCCTG
GTGAAGTCGATGATGATTTAGAACCTGAAGTAAAAGACGAATGCACTACAAAATATGGAG
AAGTTGTCACTGTTCATATCATGGAAATGCCTAATCAAATACCAGAAGAAACAGTAAGAA
TTTTTGTAGAATTCAGTCGAATTGAAAGCGCAATCAAAGCATTAGTTGATTTAAATGGAA
GATTTTTTGGAGGACGTCAAGTAAGATGTCGATTTTATTCATCTGAAAAATATGAAAACT
TTATATTTAATGAATAA

>g6229.t2 Gene=g6229 Length=178
MAKYGFKDGQGLGKQEQGISSALQVEKTSKRGGRIISEKEVKEMSTITQTPQQQQAQPEP
QTSQNPSLPSEQSITEMMKNPSKVILLRNMVGPGEVDDDLEPEVKDECTTKYGEVVTVHI
MEMPNQIPEETVRIFVEFSRIESAIKALVDLNGRFFGGRQVRCRFYSSEKYENFIFNE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6229.t2 CDD cd12647 RRM_UHM_SPF45 81 174 3.62617E-51
5 g6229.t2 Gene3D G3DSA:3.30.70.330 - 79 176 2.0E-27
12 g6229.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 76 -
11 g6229.t2 MobiDBLite mobidb-lite consensus disorder prediction 42 76 -
3 g6229.t2 PANTHER PTHR13288 SPLICING FACTOR 45 SPF45 1 177 3.9E-71
6 g6229.t2 PIRSF PIRSF031066 SPF45 1 178 2.3E-82
1 g6229.t2 Pfam PF01585 G-patch domain 1 33 7.7E-10
2 g6229.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 111 162 1.5E-5
14 g6229.t2 ProSiteProfiles PS50174 G-patch domain profile. 1 39 11.929
13 g6229.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 83 168 10.548
9 g6229.t2 SMART SM00443 G-patch_5 1 37 8.3E-4
8 g6229.t2 SMART SM00361 rrm2_1 84 164 4.9E-18
10 g6229.t2 SMART SM00360 rrm1_1 84 164 4.9E-5
4 g6229.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 86 170 1.76E-16

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:0043484 regulation of RNA splicing BP
GO:0003676 nucleic acid binding MF

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.

Raw TPM values