General information for g1019.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein fork head.
Parent gene
- The parent gene g1019 is located on chr_3: 7501643..7503025 (+ 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_3 | g1019 | g1019.t1 | TSS | g1019.t1 | 7500913 | 7500913 |
| chr_3 | g1019 | g1019.t1 | isoform | g1019.t1 | 7501643 | 7503025 |
| chr_3 | g1019 | g1019.t1 | exon | g1019.t1.exon1 | 7501643 | 7503025 |
| chr_3 | g1019 | g1019.t1 | cds | g1019.t1.CDS1 | 7501643 | 7503025 |
| chr_3 | g1019 | g1019.t1 | TTS | g1019.t1 | NA | NA |
Sequences
>g1019.t1 Gene=g1019 Length=1383
ATGAAAGTGGAGGACGAGTTAAGAGCCATGCAAAAACTCTACGCAGAGACACCGATAAGT
AGTTCGGGTATGGTGAACCCGAATAATAATAATAACAACAATCCCAATACAAACAACGGA
AATTTAAGTCCAATGACTCCAACATATACAATGAATACGATGGGAATGACTGGTATGTCA
TCAGTATCACCACAAGGAAACGGTGGTGGTTCATTTGGCAGTAATGGCGCATTGGCAGCT
TCAAATATGAGCGCTATGAATTCTGCAATGAATGCGATGAATGGAAATTGCCTCACATCG
ACGCCAATTGGATATGGCTCGTTAGGTTCACCATTGGGAAATATGAGCTCTTGCATGGGT
TCAGGTATGGGCACAATGGCTCCAATGTCACAATATACATCAATGGGAAGTCGTGAACTA
ACAGAGCCGGGCTCACCAAATTCAGCCATTTTACAAAGAGCGCGCGCTGAAAAACCAACA
ACATACAGACGCAGTTATACACATGCTAAGCCACCATACAGTTACATCTCATTGATCACA
ATGGCCATACAAAATAATCCACATAAGATGCTTACATTAGCTGAAATTTATCAGTTCATT
ATGGATCTTTTTCCATTCTATCGTCAAAATCAACAAAGATGGCAAAATTCAATTCGTCAT
TCACTAAGTTTCAATGATTGCTTTGTAAAAGTTCCAAGAACGCCTGATAAACCTGGAAAA
GGTTCATTTTGGACACTTCATCCAGATTCAGGAAATATGTTTGAAAATGGCTGCTATTTG
CGAAGACAGAAGCGATTTAAAGATGATAAAAAGGAAGCGATTAGACAAATGCACAAGAGT
CCATCGAATAGTATTGAAAATCATAGTCCGCAAGGCAAGAAAGATTTGCACGATGATCAC
CATCATCACAGAGATCATACGCATCATAAGGGCATTCCTGAAGCCCACATGCTGAACTCT
GTTCATGGTAAAGATGCAGATACTTTAGCTATGCTTCACGCTACCGCAGACTTATGCTTA
GCTCAACAATCTCATTCACATTCACAGCATGGTACGCATCACCATCATCAGCAATTGCAG
CAGGAGGATATTGCTACTATGGTCAATAGATGCCATCCGTCGCTGTTAGGCGACTATCAT
TCAATGCACCATTTGAAGCAGGAACCAAGCGGTCATTTTACACCTTCAAATCATCCCTTT
TCGATAACTCGACTGCTGCCCACAGAATCGAAAGCTGATATTAAAATGTATGAGATGAGT
CAATATGCCGGTTATAATGGAATCAGTCCACTGCCTAATTCGCATGCGGCTGCCGCATTA
GGTCAAGATTCCTATTATCAAAGTTTAGGATATCATCCATCAGCCGGTACTACAAGCTTG
TGA
>g1019.t1 Gene=g1019 Length=460
MKVEDELRAMQKLYAETPISSSGMVNPNNNNNNNPNTNNGNLSPMTPTYTMNTMGMTGMS
SVSPQGNGGGSFGSNGALAASNMSAMNSAMNAMNGNCLTSTPIGYGSLGSPLGNMSSCMG
SGMGTMAPMSQYTSMGSRELTEPGSPNSAILQRARAEKPTTYRRSYTHAKPPYSYISLIT
MAIQNNPHKMLTLAEIYQFIMDLFPFYRQNQQRWQNSIRHSLSFNDCFVKVPRTPDKPGK
GSFWTLHPDSGNMFENGCYLRRQKRFKDDKKEAIRQMHKSPSNSIENHSPQGKKDLHDDH
HHHRDHTHHKGIPEAHMLNSVHGKDADTLAMLHATADLCLAQQSHSHSQHGTHHHHQQLQ
QEDIATMVNRCHPSLLGDYHSMHHLKQEPSGHFTPSNHPFSITRLLPTESKADIKMYEMS
QYAGYNGISPLPNSHAAAALGQDSYYQSLGYHPSAGTTSL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1019.t1 | CDD | cd00059 | FH | 170 | 247 | 5.91774E-52 |
| 10 | g1019.t1 | Gene3D | G3DSA:1.10.10.10 | winged helix repressor DNA binding domain | 168 | 269 | 7.9E-46 |
| 15 | g1019.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 267 | 314 | - |
| 4 | g1019.t1 | PANTHER | PTHR11829 | FORKHEAD BOX PROTEIN | 33 | 447 | 4.2E-97 |
| 5 | g1019.t1 | PANTHER | PTHR11829:SF195 | HEPATOCYTE NUCLEAR FACTOR 3-ALPHA | 33 | 447 | 4.2E-97 |
| 6 | g1019.t1 | PRINTS | PR00053 | Fork head domain signature | 170 | 183 | 8.9E-24 |
| 8 | g1019.t1 | PRINTS | PR00053 | Fork head domain signature | 191 | 208 | 8.9E-24 |
| 7 | g1019.t1 | PRINTS | PR00053 | Fork head domain signature | 214 | 231 | 8.9E-24 |
| 3 | g1019.t1 | Pfam | PF08430 | Forkhead N-terminal region | 40 | 169 | 3.4E-12 |
| 2 | g1019.t1 | Pfam | PF00250 | Forkhead domain | 170 | 255 | 2.8E-37 |
| 1 | g1019.t1 | Pfam | PF09354 | HNF3 C-terminal domain | 397 | 435 | 2.3E-4 |
| 14 | g1019.t1 | ProSitePatterns | PS00657 | Fork head domain signature 1. | 170 | 183 | - |
| 13 | g1019.t1 | ProSitePatterns | PS00658 | Fork head domain signature 2. | 214 | 220 | - |
| 16 | g1019.t1 | ProSiteProfiles | PS50039 | Fork head domain profile. | 170 | 264 | 39.456 |
| 12 | g1019.t1 | SMART | SM00339 | forkneu4 | 168 | 258 | 2.1E-59 |
| 9 | g1019.t1 | SUPERFAMILY | SSF46785 | Winged helix DNA-binding domain | 169 | 264 | 9.07E-40 |
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:0019904 | protein domain specific binding | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| GO:0043565 | sequence-specific DNA binding | MF |
| GO:0008134 | transcription factor binding | MF |
| GO:0003700 | DNA-binding transcription factor activity | MF |
KEGG
Orthology
- This transcript has been annotated with K08035 (forkhead box protein A2, hepatocyte nuclear factor 3-beta)
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. There were no conditions that were differentially expressed