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.t7 TTS g11872.t7 18881827 18881827
chr_1 g11872 g11872.t7 isoform g11872.t7 18882010 18883225
chr_1 g11872 g11872.t7 exon g11872.t7.exon1 18882010 18882070
chr_1 g11872 g11872.t7 cds g11872.t7.CDS1 18882010 18882070
chr_1 g11872 g11872.t7 exon g11872.t7.exon2 18882129 18882259
chr_1 g11872 g11872.t7 cds g11872.t7.CDS2 18882129 18882259
chr_1 g11872 g11872.t7 exon g11872.t7.exon3 18882316 18882483
chr_1 g11872 g11872.t7 cds g11872.t7.CDS3 18882316 18882483
chr_1 g11872 g11872.t7 exon g11872.t7.exon4 18882536 18882755
chr_1 g11872 g11872.t7 cds g11872.t7.CDS4 18882536 18882755
chr_1 g11872 g11872.t7 exon g11872.t7.exon5 18882806 18883128
chr_1 g11872 g11872.t7 cds g11872.t7.CDS5 18882806 18883128
chr_1 g11872 g11872.t7 exon g11872.t7.exon6 18883190 18883225
chr_1 g11872 g11872.t7 cds g11872.t7.CDS6 18883190 18883225
chr_1 g11872 g11872.t7 TSS g11872.t7 18883566 18883566

Sequences

>g11872.t7 Gene=g11872 Length=939
ATGTCTACAGAAAGTAGCTTGATAAAAATTGATATTGAATGGGGACATGAACGTCTAGTT
AGAGCTCAACAAACCGTTGAATTACGTCCATACGATATAGAATCTTGGTCAATTTTATTG
AGAGAAGCACAATCGAGAAACTGCAATGAAGTTAGATCGCTTTATGAATCTCTTGTTTCT
GTATTTCCCACAACTGCACGTTATTGGAAGATTTATATTGAGCAGGAAATGAAAGCTCGT
AATTTTGAGAGAGTAGAAAAACTTTTTCAAAGATGCTTAGTAAAAATTTTGAACATTGAT
CTTTGGAAGCTATATTTGACATATGTAAAAGAAAACAAGGCTGGATTGAGTACTCATAAA
GAGAAACTGGCACAAGCATACGATTTTGCACTTGAAAAAATTGGAATGGATCTTCATTCA
TATTCAATTTGGTCGGACTATATTGTATTTCTAAAAAGTTTTGAACCTATTGGTAGTTTT
GCGGAAAATCAACAAATTACTGCTATTCGAAGGGTTTATCAAAAAGCGGTTCTTACGCCA
ATAATCGGAATCGAAGTTCTTTGGAAGGAGTATATACAGTTTGAGCACAAAATTAATCCA
GTTATTTCGGAAAAGATGAGTTTGGAACGATCTCGTGATTACATGAATGCACGTCGTGTA
GCAAAAGAACTTGAGCATATTACAAAAGGTTTGAACAAAAACTTACCAGCCGTTCAACCT
ACTTTAACTAAAGAAGAATTTAAACAAGCTGAATTATGGAGAAAATTCATTAATTTTGAA
AAATCAAATCCTTTAAGAAGTGAAGATACAGCTCTCGTATCAAGACGAGTAATGTTTGCA
ACTGAACAATGTCTACTTGTAATGTGTCATCATCCATCTTTCTGGATAATGGCCGCTCAA
TATTTGGACAGTACAGCTAAACATTTAACAGAGAAAGCA

>g11872.t7 Gene=g11872 Length=313
MSTESSLIKIDIEWGHERLVRAQQTVELRPYDIESWSILLREAQSRNCNEVRSLYESLVS
VFPTTARYWKIYIEQEMKARNFERVEKLFQRCLVKILNIDLWKLYLTYVKENKAGLSTHK
EKLAQAYDFALEKIGMDLHSYSIWSDYIVFLKSFEPIGSFAENQQITAIRRVYQKAVLTP
IIGIEVLWKEYIQFEHKINPVISEKMSLERSRDYMNARRVAKELEHITKGLNKNLPAVQP
TLTKEEFKQAELWRKFINFEKSNPLRSEDTALVSRRVMFATEQCLLVMCHHPSFWIMAAQ
YLDSTAKHLTEKA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11872.t7 Gene3D G3DSA:1.25.40.1040 - 15 313 0.0e+00
1 g11872.t7 PANTHER PTHR19980 RNA CLEAVAGE STIMULATION FACTOR 18 307 0.0e+00
4 g11872.t7 SMART SM00386 hat_new_1 46 78 1.2e-01
6 g11872.t7 SMART SM00386 hat_new_1 80 111 4.5e-04
3 g11872.t7 SMART SM00386 hat_new_1 118 153 2.6e+00
5 g11872.t7 SMART SM00386 hat_new_1 164 197 5.7e-03
7 g11872.t7 SMART SM00386 hat_new_1 230 262 4.6e+01
2 g11872.t7 SUPERFAMILY SSF48452 TPR-like 22 312 0.0e+00

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