General information for g17578.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Hepatocyte nuclear factor 6.
Parent gene
- The parent gene g17578 is located on chr_4: 13998868..14001634 (- 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_4 | g17578 | g17578.t1 | TTS | g17578.t1 | 13997971 | 13997971 |
| chr_4 | g17578 | g17578.t1 | isoform | g17578.t1 | 13998868 | 14001634 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon1 | 13998868 | 13999170 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS1 | 13998868 | 13999170 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon2 | 13999232 | 13999335 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS2 | 13999232 | 13999335 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon3 | 13999410 | 13999436 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS3 | 13999410 | 13999436 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon4 | 13999692 | 13999824 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS4 | 13999692 | 13999824 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon5 | 13999894 | 13999968 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS5 | 13999894 | 13999968 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon6 | 14000032 | 14000172 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS6 | 14000032 | 14000172 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon7 | 14000225 | 14000856 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS7 | 14000225 | 14000856 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon8 | 14000913 | 14001233 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS8 | 14000913 | 14001233 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon9 | 14001291 | 14001389 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS9 | 14001291 | 14001389 |
| chr_4 | g17578 | g17578.t1 | exon | g17578.t1.exon10 | 14001454 | 14001634 |
| chr_4 | g17578 | g17578.t1 | cds | g17578.t1.CDS10 | 14001454 | 14001634 |
| chr_4 | g17578 | g17578.t1 | TSS | g17578.t1 | NA | NA |
Sequences
>g17578.t1 Gene=g17578 Length=2016
ATGGAATCGATAGAAGAAATAATTGAACAAGAGATTGTGGAACCGTTGGTAGAAGAAACA
CATCATGCACATCATATACAATCACATCGCAATCATCGACATCATAACAATGGTTCAATT
GTTATTACAACACAAGCAGGACAAATTTTGCATCGCACTGGACATGAATTAAATAATAAT
GAGCAATTAGATCATCAACGTGGTCGAATCATTACACATGCAAGCCAGGTTGTACCTGGA
TTAGAAATGATAAAACAAGAACATCCTTGTTCTGATTTAGATACTCAACTTGACCATCAT
TCAGTACAACACCATCATCAAAAACAAGAAACTTTATCGGTAATTGTACAACCACACGAT
GATTCACGTGATTCAACACAACAAATTTTAAGTCCCGACTCTGGACCATGCACTGAAATT
ATTGATGCATCAGATTTCCGTTCAATGAATGAGCCAACTTATCAAACTTTGACATCAGTT
AATGGGAGAATGTCACCACCTGGATTTAGTCCAAATTCTAGTTATGCTACTTTAACACCT
CTTACGCCTCTTCCTCCAATTTCAACAATGTCAGATAAATTTGCATACGGACATGCTCAC
GGTCTTGGTGGTGTTAACTCACCATATACGTATGACGATAAGTCACCATCAATGGACATA
TCACCACCTCACAGCTACTCGCCTATTCCTCAATCCATCTACAGCCAAAATGGCCTTCCA
TCACCACCTCAAAAGAGCATGTCACCTGTTTATGAATCACCATATAGTAATCATCGAGAT
TTGCTTGGATCTTCTACTGCACCAACATCATCACGACAACAAAATGGTAATGGAGTTATA
AGCGATCATCAAACATCACCAACTTCACCACCGCATAGCTTTTCACCACAATCCATGTAT
AATGGGATTCGTCAAAATGGTAATAGTCAACAACAGCAACAACAAAACATTTCAATTACA
ACATCAGCACCAAGTCCAACTTTAAGTGCACAATCAGCTGAATTGCATTCACCAGTTGAG
CAAATTGATAAACTTTGGAATGGAAAAATGATGGAATCATCATCAAATATACATCATAAT
GGTTCGCAGTCAGCATTTGTTCAAATGAGTGGCAACAACAATAATAGCGGAAATCTTCAC
ATGACACAACAGCAACATCATCATCACAATCAAAATAATCGTGAGCTTCTCAGCAGCAGC
AGTGTTTCTCCAATAACGCCACTTATTCAGAGGGGAGGAGACAATACTGGAAGCAATAGC
AATGCAACACCTAATGCAATAACAAATAAAAGCAGCAGCAAATTGTCATCAAGTAATGCT
TCGCTGTCGTTATCAAGCGATGTTGAAGAAATAAACACAAAAGAATTGGCACAGCGTATT
AGTGCTGAATTAAAGCGTTATAGCATTCCGCAAGCAATTTTTGCCCAACGTGTCTTGTGC
CGTTCACAGGGTACTTTATCAGATCTATTAAGGAATCCAAAACCATGGTCAAAATTGAAA
TCAGGTCGTGAAACATTCAGACGAATGGCAAAATGGTTGCAAGAACCAGAATATCAAAGG
ATGAGTGCTCTAAGATTAGCAGCTGCTCAGATACCACAGCGTGGTGGAAACAGCTGTAAG
CGAAAGGAGGAAAATGATCATGTTCAAACGCCAAAGAAACCAAGATTGGTGTTTACTGAT
TTACAAAGACGTACCTTACAAGCAATATTTAAAGAAACAAAGAGACCTAGCAAAGAAATG
GTCGTCACAATCGCGAGACAGCTCTGTCTACAAGCAACTACTGTAGGTAACTTTTTCATG
AATTCTCGTCGTCGATCAAGTGACAAATGGCAAGAGGAAACACATGATGACAATGAAGAC
AATGATGGAAATGAAGATGATGAAGACGATGATGATGAAGACGATGAATGTCATATGGAT
GCAGTTCAGCAGCAAGCAACAAAACAACAAATTCAATATCACTTGCAACAACATCATGCA
CAGCAGCAAGCACAAGCAGCACATGACGAGATGTGA
>g17578.t1 Gene=g17578 Length=671
MESIEEIIEQEIVEPLVEETHHAHHIQSHRNHRHHNNGSIVITTQAGQILHRTGHELNNN
EQLDHQRGRIITHASQVVPGLEMIKQEHPCSDLDTQLDHHSVQHHHQKQETLSVIVQPHD
DSRDSTQQILSPDSGPCTEIIDASDFRSMNEPTYQTLTSVNGRMSPPGFSPNSSYATLTP
LTPLPPISTMSDKFAYGHAHGLGGVNSPYTYDDKSPSMDISPPHSYSPIPQSIYSQNGLP
SPPQKSMSPVYESPYSNHRDLLGSSTAPTSSRQQNGNGVISDHQTSPTSPPHSFSPQSMY
NGIRQNGNSQQQQQQNISITTSAPSPTLSAQSAELHSPVEQIDKLWNGKMMESSSNIHHN
GSQSAFVQMSGNNNNSGNLHMTQQQHHHHNQNNRELLSSSSVSPITPLIQRGGDNTGSNS
NATPNAITNKSSSKLSSSNASLSLSSDVEEINTKELAQRISAELKRYSIPQAIFAQRVLC
RSQGTLSDLLRNPKPWSKLKSGRETFRRMAKWLQEPEYQRMSALRLAAAQIPQRGGNSCK
RKEENDHVQTPKKPRLVFTDLQRRTLQAIFKETKRPSKEMVVTIARQLCLQATTVGNFFM
NSRRRSSDKWQEETHDDNEDNDGNEDDEDDDDEDDECHMDAVQQQATKQQIQYHLQQHHA
QQQAQAAHDEM
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g17578.t1 | CDD | cd00086 | homeodomain | 552 | 606 | 1.42811E-10 |
| 10 | g17578.t1 | Gene3D | G3DSA:1.10.260.40 | - | 448 | 526 | 1.0E-39 |
| 9 | g17578.t1 | Gene3D | G3DSA:1.10.10.60 | - | 536 | 603 | 1.1E-21 |
| 18 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 265 | 294 | - |
| 20 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 306 | 336 | - |
| 16 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 381 | 400 | - |
| 17 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 533 | 552 | - |
| 15 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 537 | 552 | - |
| 21 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 603 | 671 | - |
| 19 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 617 | 638 | - |
| 14 | g17578.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 642 | 664 | - |
| 3 | g17578.t1 | PANTHER | PTHR14057:SF9 | HEPATOCYTE NUCLEAR FACTOR 6 | 135 | 200 | 1.1E-91 |
| 5 | g17578.t1 | PANTHER | PTHR14057 | TRANSCRIPTION FACTOR ONECUT | 135 | 200 | 1.1E-91 |
| 4 | g17578.t1 | PANTHER | PTHR14057:SF9 | HEPATOCYTE NUCLEAR FACTOR 6 | 431 | 619 | 1.1E-91 |
| 6 | g17578.t1 | PANTHER | PTHR14057 | TRANSCRIPTION FACTOR ONECUT | 431 | 619 | 1.1E-91 |
| 2 | g17578.t1 | Pfam | PF02376 | CUT domain | 449 | 523 | 1.2E-32 |
| 1 | g17578.t1 | Pfam | PF00046 | Homeodomain | 552 | 605 | 5.5E-10 |
| 23 | g17578.t1 | ProSiteProfiles | PS51042 | CUT domain profile. | 442 | 528 | 29.802 |
| 22 | g17578.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 549 | 609 | 11.904 |
| 12 | g17578.t1 | SMART | SM01109 | CUT_2 | 443 | 528 | 3.0E-43 |
| 13 | g17578.t1 | SMART | SM00389 | HOX_1 | 551 | 613 | 9.0E-10 |
| 7 | g17578.t1 | SUPERFAMILY | SSF47413 | lambda repressor-like DNA-binding domains | 439 | 528 | 2.01E-35 |
| 8 | g17578.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 551 | 612 | 3.21E-12 |
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:0003677 | DNA binding | MF |
KEGG
Orthology
- This transcript has been annotated with K08026 (one cut domain, family member 1 (hepatocyte nuclear factor 6))
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