Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Nuclear transcription factor Y subunit beta.

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 g5893 g5893.t1 TSS g5893.t1 12630883 12630883
chr_2 g5893 g5893.t1 isoform g5893.t1 12630979 12631488
chr_2 g5893 g5893.t1 exon g5893.t1.exon1 12630979 12631042
chr_2 g5893 g5893.t1 cds g5893.t1.CDS1 12630979 12631042
chr_2 g5893 g5893.t1 exon g5893.t1.exon2 12631100 12631488
chr_2 g5893 g5893.t1 cds g5893.t1.CDS2 12631100 12631488
chr_2 g5893 g5893.t1 TTS g5893.t1 12631586 12631586

Sequences

>g5893.t1 Gene=g5893 Length=453
ATGAATTCTTCAGATCAGTTTGAAATAATTGATGGATATGTTCAGGATGATTCTTCAGAA
CCAGAAACAGGATTTTTAAGAGAACAAGATAGGTTTCTGCCTATAGCAAATATTGCTAAA
ATAATGAAGAAAGCAATTCCTAATAACAGTCAAGGAAAAATTGCAAAAGATGCTCGTGAA
TGTGTACAAGAATGCGTATCAGAATTTATTAGTTTCATTACTTCAGAAGCATCAGAGAGA
TGTGCACAAGAAAAAAGAAAAACTATGAATGGAGAAGATATTCTTTGGGCAATGCAGAAT
CTTGGTTTTGATAATTACATTGAACCGTTGAAAATTTTTCTTCAAAAATATCGAGACACA
ACTAAGAGCATAGAAGTATCACGCGAAGAAACCAGCCAGAGCGATGATGCAGCTTCTTTT
AATAAGTTTTTAAATAATGGAAATCAATACTAA

>g5893.t1 Gene=g5893 Length=150
MNSSDQFEIIDGYVQDDSSEPETGFLREQDRFLPIANIAKIMKKAIPNNSQGKIAKDARE
CVQECVSEFISFITSEASERCAQEKRKTMNGEDILWAMQNLGFDNYIEPLKIFLQKYRDT
TKSIEVSREETSQSDDAASFNKFLNNGNQY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5893.t1 Gene3D G3DSA:1.10.20.10 Histone 25 146 1.0E-42
2 g5893.t1 PANTHER PTHR11064:SF9 NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT BETA 21 138 3.8E-58
3 g5893.t1 PANTHER PTHR11064 CCAAT-BINDING TRANSCRIPTION FACTOR-RELATED 21 138 3.8E-58
6 g5893.t1 PRINTS PR00615 CCAAT-binding transcription factor subunit A signature 62 80 2.8E-21
5 g5893.t1 PRINTS PR00615 CCAAT-binding transcription factor subunit A signature 81 99 2.8E-21
4 g5893.t1 PRINTS PR00615 CCAAT-binding transcription factor subunit A signature 100 118 2.8E-21
1 g5893.t1 Pfam PF00808 Histone-like transcription factor (CBF/NF-Y) and archaeal histone 32 98 3.8E-26
8 g5893.t1 ProSitePatterns PS00685 NF-YB/HAP3 subunit signature. 65 81 -
7 g5893.t1 SUPERFAMILY SSF47113 Histone-fold 29 125 3.42E-38

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5893/g5893.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5893.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific MF
GO:0016602 CCAAT-binding factor complex CC
GO:0006355 regulation of transcription, DNA-templated BP
GO:0046982 protein heterodimerization activity MF
GO:0043565 sequence-specific DNA 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