Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein suppressor of forked.

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 g11872 g11872.t9 TTS g11872.t9 18881827 18881827
chr_1 g11872 g11872.t9 isoform g11872.t9 18882010 18883225
chr_1 g11872 g11872.t9 exon g11872.t9.exon1 18882010 18882070
chr_1 g11872 g11872.t9 cds g11872.t9.CDS1 18882010 18882070
chr_1 g11872 g11872.t9 exon g11872.t9.exon2 18882129 18882259
chr_1 g11872 g11872.t9 cds g11872.t9.CDS2 18882129 18882259
chr_1 g11872 g11872.t9 exon g11872.t9.exon3 18882316 18882483
chr_1 g11872 g11872.t9 cds g11872.t9.CDS3 18882316 18882483
chr_1 g11872 g11872.t9 exon g11872.t9.exon4 18882536 18883225
chr_1 g11872 g11872.t9 cds g11872.t9.CDS4 18882536 18882709
chr_1 g11872 g11872.t9 TSS g11872.t9 18883566 18883566

Sequences

>g11872.t9 Gene=g11872 Length=1050
ATGTCTACAGAAAGTAGCTTGATAAAAATTGATATTGTAAGTGAACATTTAATCTTTCAA
AAGTAAAAATTATTTTAAAAATCATTGATAATTTTAGGAATGGGGACATGAACGTCTAGT
TAGAGCTCAACAAACCGTTGAATTACGTCCATACGATATAGAATCTTGGTCAATTTTATT
GAGAGAAGCACAATCGAGAAACTGCAATGAAGTTAGATCGCTTTATGAATCTCTTGTTTC
TGTATTTCCCACAACTGCACGTTATTGGAAGATTTATATTGAGCAGGAAATGAAAGCTCG
TAATTTTGAGAGAGTAGAAAAACTTTTTCAAAGATGCTTAGTAAAAATTTTGAACATTGA
TCTTTGGAAGCTATATTTGACATATGTAAAAGAAAACAAGGCTGGATTGAGTACTCATAA
GTATGTTATAATTTTCATTAATTGAAGATTTCTTATTATTATATTTTTAGAGAGAAACTG
GCACAAGCATACGATTTTGCACTTGAAAAAATTGGAATGGATCTTCATTCATATTCAATT
TGGTCGGACTATATTGTATTTCTAAAAAGTTTTGAACCTATTGGTAGTTTTGCGGAAAAT
CAACAAATTACTGCTATTCGAAGGGTTTATCAAAAAGCGGTTCTTACGCCAATAATCGGA
ATCGAAGTTCTTTGGAAGGAGTATATACAGTTTGAGCACAAAATTAATCCAGTTATTTCG
GAAAAGATGAGTTTGGAACGATCTCGTGATTACATGAATGCACGTCGTGTAGCAAAAGAA
CTTGAGCATATTACAAAAGGTTTGAACAAAAACTTACCAGCCGTTCAACCTACTTTAACT
AAAGAAGAATTTAAACAAGCTGAATTATGGAGAAAATTCATTAATTTTGAAAAATCAAAT
CCTTTAAGAAGTGAAGATACAGCTCTCGTATCAAGACGAGTAATGTTTGCAACTGAACAA
TGTCTACTTGTAATGTGTCATCATCCATCTTTCTGGATAATGGCCGCTCAATATTTGGAC
AGTACAGCTAAACATTTAACAGAGAAAGCA

>g11872.t9 Gene=g11872 Length=178
MDLHSYSIWSDYIVFLKSFEPIGSFAENQQITAIRRVYQKAVLTPIIGIEVLWKEYIQFE
HKINPVISEKMSLERSRDYMNARRVAKELEHITKGLNKNLPAVQPTLTKEEFKQAELWRK
FINFEKSNPLRSEDTALVSRRVMFATEQCLLVMCHHPSFWIMAAQYLDSTAKHLTEKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g11872.t9 Gene3D G3DSA:1.25.40.1040 - 1 178 0.0000
1 g11872.t9 PANTHER PTHR19980 RNA CLEAVAGE STIMULATION FACTOR 1 172 0.0000
4 g11872.t9 SMART SM00386 hat_new_1 29 62 0.0057
3 g11872.t9 SMART SM00386 hat_new_1 95 127 46.0000
2 g11872.t9 SUPERFAMILY SSF48452 TPR-like 1 177 0.0000

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:0006396 RNA processing BP
GO:0005515 protein 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