Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative SET and MYND domain-containing protein 4.

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 g5834 g5834.t1 isoform g5834.t1 12203711 12205766
chr_2 g5834 g5834.t1 exon g5834.t1.exon1 12203711 12204305
chr_2 g5834 g5834.t1 cds g5834.t1.CDS1 12203711 12204305
chr_2 g5834 g5834.t1 exon g5834.t1.exon2 12204387 12205005
chr_2 g5834 g5834.t1 cds g5834.t1.CDS2 12204387 12205005
chr_2 g5834 g5834.t1 exon g5834.t1.exon3 12205448 12205766
chr_2 g5834 g5834.t1 cds g5834.t1.CDS3 12205448 12205766
chr_2 g5834 g5834.t1 TSS g5834.t1 NA NA
chr_2 g5834 g5834.t1 TTS g5834.t1 NA NA

Sequences

>g5834.t1 Gene=g5834 Length=1533
ATGAGACTAACTAAGAGCGACGAAAAGGCAAATTTATACCGATTCGAAGGAAATAATTTT
TATAAAGCTAAAAAATTTTATGATGCAATAATAAATTATAATAAAAGTTTGTGTTTTAGT
GAAATTGAAAGTGAAAATCTAGGTTTAGCTTATGCGAATCGTTCTGCCATATGTTTTGAA
TTACGAATGTTTGACAAGTGTCTTAAAAATATTTCACTTGCACGAGCACACAACTATCCA
AAGGAAAATTCTGAAATACTTAAAAATCGTGAGAAAAAATGTTTAGAGTTTATTGCTCGT
ACAAAGTCAAGTGCGTGTAAAGAATTTTTCAAATTGTCTCATAAATGTCACGAAAAAATT
CCCTACATCGTCAATTCATTAGAAATGAAAGTGAATGAAAAATACGGTAGACATGTTGTG
ACAAATGAAGATTTACATGTTGGCGACATTGTGGCTATTGAAGAATCTTTTTGCAATGTG
CTTTTGACGCAATCAAAATTTGTTGATGTAGATCAAAATAATAATTTTTTAAGATGCAGT
TATTGCTTGAAAAGCAATGAATTTGAGCTGATTCCCTGTAAAAGTTGTTGTAGCTCAATG
TTCTGCAAAGAATGCTACAATAAAGCACAGACGAGATTTCACATATATGAATGTCCAGTG
ATTGAACAACTTTTAACTTCTGGAAGTGTTCATATTGCATTGAGAATTTTTTTCATTGCT
CTATCAGCTTTCGATGGATCAATTGAAAAATTAAAAACTTTTATGAATGAAATTGACAAA
GAAAAATCGTTGACAATTTTTGATATTGATGTGAAAGAGACAAGCAATGTTAAAAATTAT
CTGAAAGTTTTAAACTCGCTCACAAGAAGTACAACAATATTTCCACTTACACAACATGAA
ATGATTCTTCAAAGTCATCAAGAATTAAGTAAAATTTGGAATGAAAATAAAGAATTTATT
AGAGAATTTCTACAACGACAATGTCAAACAAATGATCATTATTTTCATGGTATTTTTGGT
TCTAATTTGAATGAACTTAAATCTACTGCAATCAATGATCTTCAACAGTCCATTGGATCT
GGATGGTTTCCATTTTGTAGTCTTATAAATCACTCTTGTTGCAGCAATATTATGAGAATT
TATAAAGATGGAAAAGTTGCTATAGTCGTATCAAGATTTATACTAAAAGGCTCCCAACTT
TTTGACTGTTATAAGACTAGTTTTATAAACACACCAAAAGCAGAAAGACAATTAAAATTA
CAAAGCGAATTTGGATTTCTTTGTGATTGTGAAGCTTGCGAAGGAAATTTTTCAATTTTG
CAAAAACTTCCAATAAAAGACTTGAATTTAGCAAAAGCGACGAAAAGTTTAGAAATTGAA
ATGATGATTTCTGACAATTTAAACAAGAACTATAAGAAGTTTCAAGAATGCTGTCGATTG
ATTGAAGAGCACAGAAATAAATTTCCATGTGTTGAGTTAGTGCTTTTACAAAAGTGTTTT
GCTTTTTATTTATTGCTTCAAGCTAGAAAATAG

>g5834.t1 Gene=g5834 Length=510
MRLTKSDEKANLYRFEGNNFYKAKKFYDAIINYNKSLCFSEIESENLGLAYANRSAICFE
LRMFDKCLKNISLARAHNYPKENSEILKNREKKCLEFIARTKSSACKEFFKLSHKCHEKI
PYIVNSLEMKVNEKYGRHVVTNEDLHVGDIVAIEESFCNVLLTQSKFVDVDQNNNFLRCS
YCLKSNEFELIPCKSCCSSMFCKECYNKAQTRFHIYECPVIEQLLTSGSVHIALRIFFIA
LSAFDGSIEKLKTFMNEIDKEKSLTIFDIDVKETSNVKNYLKVLNSLTRSTTIFPLTQHE
MILQSHQELSKIWNENKEFIREFLQRQCQTNDHYFHGIFGSNLNELKSTAINDLQQSIGS
GWFPFCSLINHSCCSNIMRIYKDGKVAIVVSRFILKGSQLFDCYKTSFINTPKAERQLKL
QSEFGFLCDCEACEGNFSILQKLPIKDLNLAKATKSLEIEMMISDNLNKNYKKFQECCRL
IEEHRNKFPCVELVLLQKCFAFYLLLQARK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5834.t1 Gene3D G3DSA:1.25.40.10 - 2 111 1e-07
5 g5834.t1 Gene3D G3DSA:2.170.270.10 SET domain 316 436 0e+00
2 g5834.t1 PANTHER PTHR47111 BCDNA.LD29892 4 505 0e+00
1 g5834.t1 Pfam PF00856 SET domain 136 404 1e-07
3 g5834.t1 SUPERFAMILY SSF48452 TPR-like 8 76 6e-07
4 g5834.t1 SUPERFAMILY SSF82199 SET domain 123 431 0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5834/g5834.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5834.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

Pathway

This gene does not belong to any 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. There were no conditions that were differentially expressed