General information for g10814.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIF subunit 1.
Parent gene
- The parent gene g10814 is located on chr_1: 12109342..12111929 (- 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 | g10814 | g10814.t1 | isoform | g10814.t1 | 12109342 | 12111929 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon1 | 12109342 | 12109407 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS1 | 12109342 | 12109407 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon2 | 12109468 | 12109950 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS2 | 12109468 | 12109950 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon3 | 12110022 | 12110369 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS3 | 12110022 | 12110369 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon4 | 12110442 | 12110462 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS4 | 12110442 | 12110462 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon5 | 12110851 | 12111086 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS5 | 12110851 | 12111086 |
| chr_1 | g10814 | g10814.t1 | exon | g10814.t1.exon6 | 12111140 | 12111929 |
| chr_1 | g10814 | g10814.t1 | cds | g10814.t1.CDS6 | 12111140 | 12111929 |
| chr_1 | g10814 | g10814.t1 | TSS | g10814.t1 | NA | NA |
| chr_1 | g10814 | g10814.t1 | TTS | g10814.t1 | NA | NA |
Sequences
>g10814.t1 Gene=g10814 Length=1944
ATGAAAGCTGCAAAGGATAAAATTGTGTCATCATTCTGGATTTTCCACATAATTATGATT
TCTTTTGGACTTGTTCAATTGAAACCATTGAAAAGTATCAATGCATTGATTTTTTCACGG
CTTCATATGGCAATTTTTGCAAGTGTATTAACATGGTTAATTGTGGCGAATATAAAACTT
ATGAATATCATAGTCGCAGACTCAATTGTTGATTTTTGTCAATATCTTGATAGATGCAGC
ATGAATGTCTGTATTTTATTGACATTTATTGATTCAATTGTATTTAAGAAGAAACATTTT
AAAATTTTTGAGTTAATGAGTGAAATTGATGAAAAGTTTGAAAAATGTTTGAAACTCAAA
ATTAACTACAATAATTTTGCTAAAATCACAGTTGGAATATTTGCTTTAAGTTTTTTAACA
ATTATTTATCTTATAAGACGCGGAATTGAATCAAAATTGATAAATATCGAGAATATTGTG
TTTTTTATAATATTTTGTCTAGGCGCATATTTAACAACTCTTTATGAATTATATTACTCT
GCTATTATACTACAAAATTTGTATCGACATAAGATGTTAAAAGAATTTTTAATTCATAAT
TATTGTGACATGAATAGAGAAATTGTTAATGAGATTTTTATAAAAGCTCATAAAATAATT
GATGTCATCAATGATGAATTTGGTATTTTTATGCTACTTGTCACTGTCAGACATTTCATA
AGAGTTACTACTCGCATTTATATTATATTTCATTTATTAAGTTCTGAAATCATCAATTTA
TTAGTTTTCGCCGTAATCTATTTGTTTATTGTGGAAACAGTTTTTATATTTCTTGTAAGC
TTATCTGCTGGTTTTTGCACTAACGAACTTAATGAATGTAAAAGAATTTTTATTAATCAC
GTGCTCGATCAAGATCCTAAAAAATATTCTGAAAATCAAGAATTAATTTGCTTAAGACAA
ATGCAACTTGAGACAAATTTTTCTGCTTTTGGATGCTTTGAAGTTGATTTTGGTGTCATC
AAAATTATGCATAAACCAGGACAAATCAATAATCCTAATTCTTCTTCTACACCAACGCCA
ATAATTACTGAGTATTCAATAAGAGTACCCAAAAATCTTAAGAGCAAGCATCATATTATG
AGATTTAATTACAATCTAAAAGTAGATTTTTCGCAATGGAAAAATGTTCGTATGGAAAGA
GAAAATAATATGAGAGAATTCAAGACAATGGAAGAAGAGCTACCGAAATTTGGTGCCGGT
TCAGAATATAATCGTGATCAAAAAGAGGAAGCACGTCGCAAGAAGTTTGGAATTATTGCA
AAAAAGTACAATCCAGAAGCACAACCATGGATTTTAAAAACGTCGAGTGGCAAATCAGGG
AAAAAGTTTCGAGGTATAAGAGAAGGTGGTGTGAGTGAAAATGCAGCTCATTTTGTGTTT
ACGCAAACAAAGGATGGTTCAATTGAGGCTTTTCCACTTCATGAATGGTACAATTTTCAA
CCAATTCAAAGATATAAAGCCCTTACTGCTGAAGAAGCAGAAGAAGAATTTGGTCGTCGT
CGTAAATGTGTAAATTTATGGTCAATGAAAATGCGAATGAAATTAAAGAATAAAGATGAT
GAGGAAGCAGAAGATCCTGAAGATAAACCAGTGAAGGGATCAAAAGGTGGTGATAAAAAG
AAACTTATGATTAGCGAAATGGATGAATGGATGGATTCTGATGATATGAGTTCTAGTGAT
GATGATGAAGATGGTGAAAAGAAAAAGAAAGAGGAAGAAAGTGATGACGATCAAGGTGCC
AAGAACAAGAAAGGCAAAGGAAAAGCTGCACAAAATGCCAAGAAAAAGAAACGTGACGTG
GATGATGAAGCATTTGAAGAATCTGACGATGGTGATGAAGAAGGACGAGAACGTGACTAT
ATTTCAGACTCGAGTGATAGGTAA
>g10814.t1 Gene=g10814 Length=647
MKAAKDKIVSSFWIFHIIMISFGLVQLKPLKSINALIFSRLHMAIFASVLTWLIVANIKL
MNIIVADSIVDFCQYLDRCSMNVCILLTFIDSIVFKKKHFKIFELMSEIDEKFEKCLKLK
INYNNFAKITVGIFALSFLTIIYLIRRGIESKLINIENIVFFIIFCLGAYLTTLYELYYS
AIILQNLYRHKMLKEFLIHNYCDMNREIVNEIFIKAHKIIDVINDEFGIFMLLVTVRHFI
RVTTRIYIIFHLLSSEIINLLVFAVIYLFIVETVFIFLVSLSAGFCTNELNECKRIFINH
VLDQDPKKYSENQELICLRQMQLETNFSAFGCFEVDFGVIKIMHKPGQINNPNSSSTPTP
IITEYSIRVPKNLKSKHHIMRFNYNLKVDFSQWKNVRMERENNMREFKTMEEELPKFGAG
SEYNRDQKEEARRKKFGIIAKKYNPEAQPWILKTSSGKSGKKFRGIREGGVSENAAHFVF
TQTKDGSIEAFPLHEWYNFQPIQRYKALTAEEAEEEFGRRRKCVNLWSMKMRMKLKNKDD
EEAEDPEDKPVKGSKGGDKKKLMISEMDEWMDSDDMSSSDDDEDGEKKKKEEESDDDQGA
KNKKGKGKAAQNAKKKKRDVDDEAFEESDDGDEEGRERDYISDSSDR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 29 | g10814.t1 | CDD | cd00240 | TFIIFa | 363 | 525 | 2.03117E-76 |
| 12 | g10814.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 536 | 568 | - |
| 13 | g10814.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 536 | 647 | - |
| 11 | g10814.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 582 | 604 | - |
| 3 | g10814.t1 | PANTHER | PTHR13011 | TFIIF-ALPHA | 356 | 645 | 2.5E-70 |
| 4 | g10814.t1 | PANTHER | PTHR13011:SF0 | GENERAL TRANSCRIPTION FACTOR IIF SUBUNIT 1 | 356 | 645 | 2.5E-70 |
| 1 | g10814.t1 | Pfam | PF08395 | 7tm Chemosensory receptor | 37 | 340 | 1.0E-8 |
| 2 | g10814.t1 | Pfam | PF05793 | Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) | 354 | 646 | 4.8E-105 |
| 14 | g10814.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 6 | - |
| 28 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 27 | - |
| 21 | g10814.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 28 | 32 | - |
| 27 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 33 | 55 | - |
| 17 | g10814.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 56 | 74 | - |
| 26 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 75 | 95 | - |
| 19 | g10814.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 96 | 125 | - |
| 25 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 146 | - |
| 16 | g10814.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 147 | 157 | - |
| 24 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 158 | 178 | - |
| 20 | g10814.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 179 | 226 | - |
| 23 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 227 | 248 | - |
| 15 | g10814.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 249 | 259 | - |
| 22 | g10814.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 285 | - |
| 18 | g10814.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 286 | 647 | - |
| 10 | g10814.t1 | SUPERFAMILY | SSF50916 | Rap30/74 interaction domains | 359 | 520 | 7.06E-53 |
| 5 | g10814.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 9 | 26 | - |
| 9 | g10814.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 36 | 58 | - |
| 7 | g10814.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 145 | - |
| 6 | g10814.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 160 | 182 | - |
| 8 | g10814.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 249 | 271 | - |
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:0050909 | sensory perception of taste | BP |
| GO:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0032968 | positive regulation of transcription elongation from RNA polymerase II promoter | BP |
| GO:0016021 | integral component of membrane | CC |
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
KEGG
Orthology
- This transcript has been annotated with K03138 (transcription initiation factor TFIIF subunit alpha)
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.
