General information for g11427.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as FAS-associated factor 1.
Parent gene
- The parent gene g11427 is located on chr_1: 16164432..16165898 (- 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 | g11427 | g11427.t1 | TTS | g11427.t1 | 16163284 | 16163284 |
| chr_1 | g11427 | g11427.t1 | isoform | g11427.t1 | 16163394 | 16165898 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon1 | 16163394 | 16163552 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS1 | 16163394 | 16163552 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon2 | 16163616 | 16164150 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS2 | 16163616 | 16164150 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon3 | 16164207 | 16164361 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS3 | 16164207 | 16164361 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon4 | 16164426 | 16164571 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS4 | 16164426 | 16164571 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon5 | 16164634 | 16165065 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS5 | 16164634 | 16165065 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon6 | 16165116 | 16165295 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS6 | 16165116 | 16165295 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon7 | 16165362 | 16165454 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS7 | 16165362 | 16165454 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon8 | 16165544 | 16165634 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS8 | 16165544 | 16165634 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon9 | 16165724 | 16165792 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS9 | 16165724 | 16165792 |
| chr_1 | g11427 | g11427.t1 | exon | g11427.t1.exon10 | 16165854 | 16165898 |
| chr_1 | g11427 | g11427.t1 | cds | g11427.t1.CDS10 | 16165854 | 16165898 |
| chr_1 | g11427 | g11427.t1 | TSS | g11427.t1 | 16166022 | 16166022 |
Sequences
>g11427.t1 Gene=g11427 Length=1905
ATGGAGGAAGTTTTAAATAAAGAGGAAATTCTTGCAAACTTTCAGCAAATCACTGCAATT
GAGGATATTGGAATAGCTCTAAGTCATTTAGAGTCAACAGGATGGGATTTAGAGACTGCA
GTGAGGATTGCTATACTGATGGATGGAAATGAAAATGAAAGTATTTCTATTGTGGATAAT
GATCAAAGTGTTATAGAAGTAGCAGGTCCTTCAACTTCTACGCAGTCAGAATTGACATTC
AACATTCGCTTTAAAAAGGATTTGATTACAATAAAACTTTCTGAGTTACAGACTGTAGGA
GAATTGAAGCAGCTAATAATGAAGAAAACATCTGTTCCCGTGTGTCGACAAAATCTGAAA
ATGAATAATATACCTATTAGAAGTATGCAGTCTGATTCAACCAAATTAAAAGCTCTTAAT
TTCAACTCAAATGACATCAATTTAGAATTAACCGATATAAGTAATGATGGTGAATTAGGT
ATTGCTGCTGATATTATTCCAATTTCACCTACATCAAACTCGAATGGAAATTATCAATTA
AGAATATATTTAACAAATGAAAATCGATATTTGAATTTAAATTTTGCTCCATCAAAAACA
TTACTTGAAATCAAGAATGATGTGTTTGCAGTCTTAAAAACCCCAGTTCGATTTCAAGTT
TGGGAAGGATGGCCGTCAAATGCAACAAATGATTCTAAACTAAGCGATTTAGACATCGAT
CACATTCATTGTCTTCAATTAACATGTACTGGTAGCGATAGTGCAAGTGCAAGTAGTAGC
TCAATCAGAACAATAGGAGAAACTTTAGAAATAGATTCTGATTCTGACTCGATTGAATTT
GAGGATGCAACAGCCGATGAAGACATGTTTACAGAAGAAGGCGTTCAACCTAACCGATTA
AAACATCTAATTGAAGATGGTATTGAAGACACAGTCTTGGGATCTCTACAATTTGTAAGT
AATTACAGAGAGCGATATGGTGTTGGTCCAACTTTTTTCGAAGGTAGCTTAGAAGATGCT
CTTAAAACAGCTTATACAGCAAAATCGGCCAAGGATCGAAAATTACTTGCAATTTATTTG
CATCATGATAATAGCGTACTATCAAATGTATTTTGTGGACAGTTGTTGGGAAACGAAAAT
ATCATAAAATTATTGAATGAAAATTACATTTTATTTGGCTGGGATCTTACATTCGAATCA
AATAAAAATTTATTTTTATCGTCTTTAACTGCTTCAGCTACAGACTCGGCGTCTCTTCAA
ATTCGTAATATGGCTATTAATCAATTTCCAATTATATTAATAATCCGAAAATTTAGAGGG
ATGTGTGAAATAGCTGATATTATTCACGGAAATATTAATCGTGATGAACTGTATATTCAT
TTAATGATGAATTCAGATGCGTTTAACGAACAAATGAAAATAGATATTCGTGAAGAAAAT
GAGCGTGCTGCCAGAGAAAGTTTACTGCTAGAGCAGCAGCAAGCATATCAAGAAAGTTTG
CTAGCTGATAGAGCAAAAGAAGAGGAACGATTAAGACTTGAAAAAATGATGGAGAATGAA
CGTCAAAAACAAGAATCTGAATTAGCTGATAAACTAGCAAAAAAAGAAGCTGATAGAAGA
GATGCAGAAAATTCATTACCACCTGAGCCTACAAATGATTGCACTCAACAAATTACAAAG
ATTCGTTTTAGAAAACCAACTGGTGATTTTATTGAACGAAAATTTACAGTTGACACTCAA
TTAAAAGTTTTATTAAACTTTTCAAAAGCTAATGGATTTTCTCCAGAAGACTTTAAAATT
ATCTCAAGTTTTCCCCGACGTGATCTTACAACCATCGATTCAGCAAATACTTTAAAGCAA
TTAAATTTGTATCCACAAGAAACTCTTATATTAGAAGAACGATAA
>g11427.t1 Gene=g11427 Length=634
MEEVLNKEEILANFQQITAIEDIGIALSHLESTGWDLETAVRIAILMDGNENESISIVDN
DQSVIEVAGPSTSTQSELTFNIRFKKDLITIKLSELQTVGELKQLIMKKTSVPVCRQNLK
MNNIPIRSMQSDSTKLKALNFNSNDINLELTDISNDGELGIAADIIPISPTSNSNGNYQL
RIYLTNENRYLNLNFAPSKTLLEIKNDVFAVLKTPVRFQVWEGWPSNATNDSKLSDLDID
HIHCLQLTCTGSDSASASSSSIRTIGETLEIDSDSDSIEFEDATADEDMFTEEGVQPNRL
KHLIEDGIEDTVLGSLQFVSNYRERYGVGPTFFEGSLEDALKTAYTAKSAKDRKLLAIYL
HHDNSVLSNVFCGQLLGNENIIKLLNENYILFGWDLTFESNKNLFLSSLTASATDSASLQ
IRNMAINQFPIILIIRKFRGMCEIADIIHGNINRDELYIHLMMNSDAFNEQMKIDIREEN
ERAARESLLLEQQQAYQESLLADRAKEEERLRLEKMMENERQKQESELADKLAKKEADRR
DAENSLPPEPTNDCTQQITKIRFRKPTGDFIERKFTVDTQLKVLLNFSKANGFSPEDFKI
ISSFPRRDLTTIDSANTLKQLNLYPQETLILEER
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g11427.t1 | CDD | cd01771 | UBX_UBXN3A | 555 | 634 | 1.13946E-32 |
| 14 | g11427.t1 | Coils | Coil | Coil | 506 | 545 | - |
| 12 | g11427.t1 | Gene3D | G3DSA:1.10.8.10 | DNA helicase RuvA subunit | 4 | 45 | 3.3E-14 |
| 9 | g11427.t1 | Gene3D | G3DSA:3.10.20.90 | - | 77 | 150 | 1.1E-12 |
| 10 | g11427.t1 | Gene3D | G3DSA:3.10.20.90 | - | 179 | 247 | 4.7E-7 |
| 13 | g11427.t1 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 303 | 476 | 6.3E-45 |
| 11 | g11427.t1 | Gene3D | G3DSA:3.10.20.90 | - | 552 | 634 | 5.6E-27 |
| 18 | g11427.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 517 | 546 | - |
| 19 | g11427.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 517 | 556 | - |
| 3 | g11427.t1 | PANTHER | PTHR23322:SF56 | FAS-ASSOCIATED FACTOR 1 | 7 | 633 | 2.1E-117 |
| 4 | g11427.t1 | PANTHER | PTHR23322 | FAS-ASSOCIATED PROTEIN | 7 | 633 | 2.1E-117 |
| 2 | g11427.t1 | Pfam | PF14555 | UBA-like domain | 8 | 41 | 7.3E-7 |
| 1 | g11427.t1 | Pfam | PF00789 | UBX domain | 558 | 633 | 5.5E-12 |
| 20 | g11427.t1 | ProSiteProfiles | PS50033 | UBX domain profile. | 554 | 631 | 17.446 |
| 17 | g11427.t1 | SMART | SM00594 | 45neu3 | 317 | 462 | 1.8E-41 |
| 16 | g11427.t1 | SMART | SM00166 | ubx_3 | 550 | 633 | 2.5E-10 |
| 7 | g11427.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 70 | 144 | 1.69E-8 |
| 8 | g11427.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 172 | 248 | 4.85E-5 |
| 5 | g11427.t1 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 330 | 440 | 4.03E-5 |
| 6 | g11427.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 522 | 633 | 3.31E-22 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K20703 (FAS-associated factor 1)
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.
