General information for g11889.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Nuclear transcription factor Y subunit gamma.
Parent gene
- The parent gene g11889 is located on chr_1: 19008422..19009458 (+ strand)
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 | g11889 | g11889.t3 | TSS | g11889.t3 | 19008354 | 19008354 |
| chr_1 | g11889 | g11889.t3 | isoform | g11889.t3 | 19008422 | 19009458 |
| chr_1 | g11889 | g11889.t3 | exon | g11889.t3.exon1 | 19008422 | 19009084 |
| chr_1 | g11889 | g11889.t3 | cds | g11889.t3.CDS1 | 19008422 | 19009084 |
| chr_1 | g11889 | g11889.t3 | exon | g11889.t3.exon2 | 19009149 | 19009317 |
| chr_1 | g11889 | g11889.t3 | cds | g11889.t3.CDS2 | 19009149 | 19009317 |
| chr_1 | g11889 | g11889.t3 | exon | g11889.t3.exon3 | 19009412 | 19009458 |
| chr_1 | g11889 | g11889.t3 | cds | g11889.t3.CDS3 | 19009412 | 19009455 |
| chr_1 | g11889 | g11889.t3 | TTS | g11889.t3 | 19009449 | 19009449 |
Sequences
>g11889.t3 Gene=g11889 Length=879
ATGGATGCATCAACGTCAAAGGATGAGAAATTAACTGAAACACAGTTAGAGTTACAAAAT
TTTTTCCCAAAAGTTCTTGAGGAAATCAAAAAAATTAAAGTAATTGAGCCCGGAAATCAA
CTTTTGCCTCTTGCGCGTATAAAGAAAATAATGAAGTTAGATGAAGATGTGAAAATGATA
TCAGCTGAAGCACCATTGTTATTTGCAAAAGCAACAGAAATATTCATACATGAATTAACG
CTTAGAGCTTGGTTGCATACTGAAGATAATAAAAGAAGAACTCTTCAGAGAAATGATATC
GCTATGGCGATTTCGAAATACGATCAATTTGATTTTTTAATCGATATTGTACCAAGAGAT
GAAATCAAACCAAAAAAAGAAGCAGAAAATAAATCTACAGTTCAAGAAGTGTTTTATGTT
CAAGCACCAGGACAGCAATTGCAAACAGTTGCAGTTCCAGCAGTCCAGGCTACACCGCAA
GCAGCAACAGCACAAGCAATACAATTACCAAATGGTATTCAGGCGGCACCTGCACAAAAT
ATCATTTTACAAAGTCCAACACAAACGCAAACAACAGTACCTATAATGTTAGGAAATCCA
GGACAGCAAATTCAATTAGTGCAGCAAGTTATTGGACCAAATGGTGAAATATCACAAATA
CCTGTTCAAATGTCACAACAGCAACTTTCATTACTTCGCTCTCAGATGACTGGAACTCCA
CTCATTGTAGCACCTCAAACAATTTTCCAAACACAAGCAGGTCAAAATATTGCTATACCA
TTAAATATTGGTCAGCAATATGTAATTAATCCTCAAACGGCGATTCAACAACTTGTGAAT
AATAAAAATCATGTAAATTGTAAAATAATAAATTAAAAT
>g11889.t3 Gene=g11889 Length=291
MDASTSKDEKLTETQLELQNFFPKVLEEIKKIKVIEPGNQLLPLARIKKIMKLDEDVKMI
SAEAPLLFAKATEIFIHELTLRAWLHTEDNKRRTLQRNDIAMAISKYDQFDFLIDIVPRD
EIKPKKEAENKSTVQEVFYVQAPGQQLQTVAVPAVQATPQAATAQAIQLPNGIQAAPAQN
IILQSPTQTQTTVPIMLGNPGQQIQLVQQVIGPNGEISQIPVQMSQQQLSLLRSQMTGTP
LIVAPQTIFQTQAGQNIAIPLNIGQQYVINPQTAIQQLVNNKNHVNCKIIN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g11889.t3 | Gene3D | G3DSA:1.10.20.10 | Histone | 4 | 119 | 0 |
| 2 | g11889.t3 | PANTHER | PTHR10252:SF8 | NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT GAMMA | 12 | 190 | 0 |
| 3 | g11889.t3 | PANTHER | PTHR10252 | HISTONE-LIKE TRANSCRIPTION FACTOR CCAAT-RELATED | 12 | 190 | 0 |
| 1 | g11889.t3 | Pfam | PF00808 | Histone-like transcription factor (CBF/NF-Y) and archaeal histone | 42 | 104 | 0 |
| 4 | g11889.t3 | SUPERFAMILY | SSF47113 | Histone-fold | 25 | 113 | 0 |
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:0016602 | CCAAT-binding factor complex | CC |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0046982 | protein heterodimerization activity | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08066 (nuclear transcription factor Y, gamma)
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.
