Gene loci information

Transcript annotation

  • This transcript has been annotated as Forkhead box protein O.

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_3 g363 g363.t1 isoform g363.t1 2974706 2995776
chr_3 g363 g363.t1 exon g363.t1.exon1 2974706 2974922
chr_3 g363 g363.t1 cds g363.t1.CDS1 2974706 2974922
chr_3 g363 g363.t1 exon g363.t1.exon2 2978558 2978763
chr_3 g363 g363.t1 cds g363.t1.CDS2 2978558 2978763
chr_3 g363 g363.t1 exon g363.t1.exon3 2992141 2992354
chr_3 g363 g363.t1 cds g363.t1.CDS3 2992141 2992354
chr_3 g363 g363.t1 exon g363.t1.exon4 2992416 2992506
chr_3 g363 g363.t1 cds g363.t1.CDS4 2992416 2992506
chr_3 g363 g363.t1 exon g363.t1.exon5 2993958 2994179
chr_3 g363 g363.t1 cds g363.t1.CDS5 2993958 2994179
chr_3 g363 g363.t1 exon g363.t1.exon6 2994505 2994658
chr_3 g363 g363.t1 cds g363.t1.CDS6 2994505 2994658
chr_3 g363 g363.t1 exon g363.t1.exon7 2995174 2995333
chr_3 g363 g363.t1 cds g363.t1.CDS7 2995174 2995333
chr_3 g363 g363.t1 exon g363.t1.exon8 2995403 2995524
chr_3 g363 g363.t1 cds g363.t1.CDS8 2995403 2995524
chr_3 g363 g363.t1 exon g363.t1.exon9 2995615 2995776
chr_3 g363 g363.t1 cds g363.t1.CDS9 2995615 2995776
chr_3 g363 g363.t1 TTS g363.t1 2996509 2996509
chr_3 g363 g363.t1 TSS g363.t1 NA NA

Sequences

>g363.t1 Gene=g363 Length=1548
ATGGATCAATATAACTCTGATCCTTGGCCATCACCACCCATTATTGAGGGACTCAATGAC
CAAATGGATTCCTTGGCAGAGCTTCAAGAAGGAGCATTTGAGCCACAAATTCGAGCTCGT
TCTAATACTTGGCCATTACCACGTCCGGAGAACTTTGTTGATCAAAATGATGATGCAGAA
AATAATCAGCAGTGTAATAATCAGCAATCTGTCACTGGAATTCCACCTACACCATCAGTG
TCAAAGAAAAATTCGTCAAGACGAAATGCATGGGGAAATTTGTCGTATGCAGATTTAATT
ACGAAAGCAATCAGTTCATCATCAGACAATAGATTAACACTGTCACAGATTTATGAATGG
ATGGTACAAAATGTTCCATACTTTAAAGACAAAGGTGATTCCAATAGCAGCGCTGGATGG
AAGAACTCAATTCGTCACAATTTGTCACTGCACAATCGATTTATGAGAGTACAAAATGAG
GGAACAGGCAAATCATCTTGGTGGATGCTTAATCCTGATGCTAAGCCTGGTAAATCAGTC
AGAAGACGAGCAGCATCCATGGAAACATCAAAGTTTGAGAAAAGACGTGGGCGAGTTAAG
AAACGCGTTGAGCAGATAAGAAATGGAGTGATAACAAATGTTTCTGGTGTGCTAAATGAT
GTCAATTCATCACCTGGCAGCAGTGTGAGCGAAGGATTGGATCTTTTTCCAGAAAGTCCC
TTGCATAGTGCAAATTTCCAATTGTCACCGGACTTTCGACAAAGAGCGAGCTCAAATGCG
AGTTCAGTGGGAAGACTGAGTCCAATTCCATCATTGGCAATTGAAAATGAATGGGATTGT
TTTGCTGAAACAGACACTGTCAATGGTAATGGTGCACCGAATCCAATTCTCGAAGACTTA
GCTGGATCACTTGCGGATGAGTTGACATTACAAAATGATTTATTTAATGGGTTCACAACA
GCGAGTCTACATCATCCACAACCACCTCCACCATACCAACCACCACAATATTCAACAATG
CACACAACAATGCCAGCTACAGTGACATATGGATTGAAACAGCCAGCACAAGCAATTCAC
ATGCTACAGAATAATACACGAGAGAGTATGTCACCTGGATCAGCAACAGGAATGTCACCA
GCATACAGTGAACCATCTCCCGACTATTCGATGCTCGTCAGTCAAAATCGACTACCGAGA
CCTTCATCAAACAGTCCGCCCCTAAATAATCTGCAAACTCTTACCACAACCCCACATATC
GGACATAACACACCTTCCACTCTAATGGGTCAATTCATTGAAGTTCTCAACAATCAAGCG
AACCTCGATGACTTGAATTTGAATTTGGAGTCATTTCAAGGTGGTTTGGATTGCAATGTC
GATGAAGTAATAAAACACGAACTCAGTTATGGTCCGTTAGATTTTAACTTTCAAAATAAC
AATCAAGATGTTATGGATGGAAGTGATGCACAACAACAGCATCCAACAGCTAACCACAAT
CATGGTCAGTATCAGCCAGCGAGAACAACCAATTCGTGGGTTCATTAA

>g363.t1 Gene=g363 Length=515
MDQYNSDPWPSPPIIEGLNDQMDSLAELQEGAFEPQIRARSNTWPLPRPENFVDQNDDAE
NNQQCNNQQSVTGIPPTPSVSKKNSSRRNAWGNLSYADLITKAISSSSDNRLTLSQIYEW
MVQNVPYFKDKGDSNSSAGWKNSIRHNLSLHNRFMRVQNEGTGKSSWWMLNPDAKPGKSV
RRRAASMETSKFEKRRGRVKKRVEQIRNGVITNVSGVLNDVNSSPGSSVSEGLDLFPESP
LHSANFQLSPDFRQRASSNASSVGRLSPIPSLAIENEWDCFAETDTVNGNGAPNPILEDL
AGSLADELTLQNDLFNGFTTASLHHPQPPPPYQPPQYSTMHTTMPATVTYGLKQPAQAIH
MLQNNTRESMSPGSATGMSPAYSEPSPDYSMLVSQNRLPRPSSNSPPLNNLQTLTTTPHI
GHNTPSTLMGQFIEVLNNQANLDDLNLNLESFQGGLDCNVDEVIKHELSYGPLDFNFQNN
NQDVMDGSDAQQQHPTANHNHGQYQPARTTNSWVH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g363.t1 CDD cd00059 FH 91 171 1.54512E-35
8 g363.t1 Gene3D G3DSA:1.10.10.10 winged helix repressor DNA binding domain 81 179 5.6E-39
13 g363.t1 MobiDBLite mobidb-lite consensus disorder prediction 66 87 -
12 g363.t1 MobiDBLite mobidb-lite consensus disorder prediction 368 388 -
14 g363.t1 MobiDBLite mobidb-lite consensus disorder prediction 487 515 -
3 g363.t1 PANTHER PTHR45767 FORKHEAD BOX PROTEIN O 26 515 1.9E-123
6 g363.t1 PRINTS PR00053 Fork head domain signature 91 104 2.8E-12
5 g363.t1 PRINTS PR00053 Fork head domain signature 112 129 2.8E-12
4 g363.t1 PRINTS PR00053 Fork head domain signature 140 157 2.8E-12
1 g363.t1 Pfam PF00250 Forkhead domain 93 175 4.0E-26
2 g363.t1 Pfam PF16676 Transactivation domain of FOXO protein family 444 478 2.9E-7
11 g363.t1 ProSitePatterns PS00658 Fork head domain signature 2. 140 146 -
15 g363.t1 ProSiteProfiles PS50039 Fork head domain profile. 91 197 25.308
10 g363.t1 SMART SM00339 forkneu4 89 178 1.8E-41
7 g363.t1 SUPERFAMILY SSF46785 Winged helix DNA-binding domain 87 173 2.4E-30

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:0006355 regulation of transcription, DNA-templated BP
GO:0043565 sequence-specific DNA binding MF
GO:0003700 DNA-binding transcription factor activity 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