Gene loci information

Transcript annotation

  • This transcript has been annotated as FAS-associated factor 1.

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_1 g11427 g11427.t2 TTS g11427.t2 16163284 16163284
chr_1 g11427 g11427.t2 isoform g11427.t2 16163394 16165898
chr_1 g11427 g11427.t2 exon g11427.t2.exon1 16163394 16163552
chr_1 g11427 g11427.t2 cds g11427.t2.CDS1 16163394 16163552
chr_1 g11427 g11427.t2 exon g11427.t2.exon2 16163616 16164150
chr_1 g11427 g11427.t2 cds g11427.t2.CDS2 16163616 16164150
chr_1 g11427 g11427.t2 exon g11427.t2.exon3 16164207 16164361
chr_1 g11427 g11427.t2 cds g11427.t2.CDS3 16164207 16164361
chr_1 g11427 g11427.t2 exon g11427.t2.exon4 16164426 16164571
chr_1 g11427 g11427.t2 cds g11427.t2.CDS4 16164426 16164571
chr_1 g11427 g11427.t2 exon g11427.t2.exon5 16164634 16165065
chr_1 g11427 g11427.t2 cds g11427.t2.CDS5 16164634 16165065
chr_1 g11427 g11427.t2 exon g11427.t2.exon6 16165125 16165295
chr_1 g11427 g11427.t2 cds g11427.t2.CDS6 16165125 16165295
chr_1 g11427 g11427.t2 exon g11427.t2.exon7 16165362 16165454
chr_1 g11427 g11427.t2 cds g11427.t2.CDS7 16165362 16165454
chr_1 g11427 g11427.t2 exon g11427.t2.exon8 16165544 16165634
chr_1 g11427 g11427.t2 cds g11427.t2.CDS8 16165544 16165634
chr_1 g11427 g11427.t2 exon g11427.t2.exon9 16165724 16165792
chr_1 g11427 g11427.t2 cds g11427.t2.CDS9 16165724 16165792
chr_1 g11427 g11427.t2 exon g11427.t2.exon10 16165854 16165898
chr_1 g11427 g11427.t2 cds g11427.t2.CDS10 16165854 16165898
chr_1 g11427 g11427.t2 TSS g11427.t2 16166022 16166022

Sequences

>g11427.t2 Gene=g11427 Length=1896
ATGGAGGAAGTTTTAAATAAAGAGGAAATTCTTGCAAACTTTCAGCAAATCACTGCAATT
GAGGATATTGGAATAGCTCTAAGTCATTTAGAGTCAACAGGATGGGATTTAGAGACTGCA
GTGAGGATTGCTATACTGATGGATGGAAATGAAAATGAAAGTATTTCTATTGTGGATAAT
GATCAAAGTGTTATAGAAGTAGCAGGTCCTTCAACTTCTACGCAGTCAGAATTGACATTC
AACATTCGCTTTAAAAAGGATTTGATTACAATAAAACTTTCTGAGTTACAGACTGTAGGA
GAATTGAAGCAGCTAATAATGAAGAAAACATCTGTTCCCGTGTGTCGACAAAATCTGAAA
ATGAATAATATACCTATTAGAAGTATGCAGTCTGATTCAACCAAATTAAAAGCTCTTAAT
TTCAACTCAAATGACATCAATTTAGAATTAACCGATATAAGTAATGATGGTATTGCTGCT
GATATTATTCCAATTTCACCTACATCAAACTCGAATGGAAATTATCAATTAAGAATATAT
TTAACAAATGAAAATCGATATTTGAATTTAAATTTTGCTCCATCAAAAACATTACTTGAA
ATCAAGAATGATGTGTTTGCAGTCTTAAAAACCCCAGTTCGATTTCAAGTTTGGGAAGGA
TGGCCGTCAAATGCAACAAATGATTCTAAACTAAGCGATTTAGACATCGATCACATTCAT
TGTCTTCAATTAACATGTACTGGTAGCGATAGTGCAAGTGCAAGTAGTAGCTCAATCAGA
ACAATAGGAGAAACTTTAGAAATAGATTCTGATTCTGACTCGATTGAATTTGAGGATGCA
ACAGCCGATGAAGACATGTTTACAGAAGAAGGCGTTCAACCTAACCGATTAAAACATCTA
ATTGAAGATGGTATTGAAGACACAGTCTTGGGATCTCTACAATTTGTAAGTAATTACAGA
GAGCGATATGGTGTTGGTCCAACTTTTTTCGAAGGTAGCTTAGAAGATGCTCTTAAAACA
GCTTATACAGCAAAATCGGCCAAGGATCGAAAATTACTTGCAATTTATTTGCATCATGAT
AATAGCGTACTATCAAATGTATTTTGTGGACAGTTGTTGGGAAACGAAAATATCATAAAA
TTATTGAATGAAAATTACATTTTATTTGGCTGGGATCTTACATTCGAATCAAATAAAAAT
TTATTTTTATCGTCTTTAACTGCTTCAGCTACAGACTCGGCGTCTCTTCAAATTCGTAAT
ATGGCTATTAATCAATTTCCAATTATATTAATAATCCGAAAATTTAGAGGGATGTGTGAA
ATAGCTGATATTATTCACGGAAATATTAATCGTGATGAACTGTATATTCATTTAATGATG
AATTCAGATGCGTTTAACGAACAAATGAAAATAGATATTCGTGAAGAAAATGAGCGTGCT
GCCAGAGAAAGTTTACTGCTAGAGCAGCAGCAAGCATATCAAGAAAGTTTGCTAGCTGAT
AGAGCAAAAGAAGAGGAACGATTAAGACTTGAAAAAATGATGGAGAATGAACGTCAAAAA
CAAGAATCTGAATTAGCTGATAAACTAGCAAAAAAAGAAGCTGATAGAAGAGATGCAGAA
AATTCATTACCACCTGAGCCTACAAATGATTGCACTCAACAAATTACAAAGATTCGTTTT
AGAAAACCAACTGGTGATTTTATTGAACGAAAATTTACAGTTGACACTCAATTAAAAGTT
TTATTAAACTTTTCAAAAGCTAATGGATTTTCTCCAGAAGACTTTAAAATTATCTCAAGT
TTTCCCCGACGTGATCTTACAACCATCGATTCAGCAAATACTTTAAAGCAATTAAATTTG
TATCCACAAGAAACTCTTATATTAGAAGAACGATAA

>g11427.t2 Gene=g11427 Length=631
MEEVLNKEEILANFQQITAIEDIGIALSHLESTGWDLETAVRIAILMDGNENESISIVDN
DQSVIEVAGPSTSTQSELTFNIRFKKDLITIKLSELQTVGELKQLIMKKTSVPVCRQNLK
MNNIPIRSMQSDSTKLKALNFNSNDINLELTDISNDGIAADIIPISPTSNSNGNYQLRIY
LTNENRYLNLNFAPSKTLLEIKNDVFAVLKTPVRFQVWEGWPSNATNDSKLSDLDIDHIH
CLQLTCTGSDSASASSSSIRTIGETLEIDSDSDSIEFEDATADEDMFTEEGVQPNRLKHL
IEDGIEDTVLGSLQFVSNYRERYGVGPTFFEGSLEDALKTAYTAKSAKDRKLLAIYLHHD
NSVLSNVFCGQLLGNENIIKLLNENYILFGWDLTFESNKNLFLSSLTASATDSASLQIRN
MAINQFPIILIIRKFRGMCEIADIIHGNINRDELYIHLMMNSDAFNEQMKIDIREENERA
ARESLLLEQQQAYQESLLADRAKEEERLRLEKMMENERQKQESELADKLAKKEADRRDAE
NSLPPEPTNDCTQQITKIRFRKPTGDFIERKFTVDTQLKVLLNFSKANGFSPEDFKIISS
FPRRDLTTIDSANTLKQLNLYPQETLILEER

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g11427.t2 CDD cd01771 UBX_UBXN3A 552 631 1.1256E-32
14 g11427.t2 Coils Coil Coil 503 542 -
12 g11427.t2 Gene3D G3DSA:1.10.8.10 DNA helicase RuvA subunit 4 45 3.3E-14
9 g11427.t2 Gene3D G3DSA:3.10.20.90 - 77 150 1.1E-12
11 g11427.t2 Gene3D G3DSA:3.10.20.90 - 176 244 4.6E-7
13 g11427.t2 Gene3D G3DSA:3.40.30.10 Glutaredoxin 300 473 6.3E-45
10 g11427.t2 Gene3D G3DSA:3.10.20.90 - 549 631 5.6E-27
18 g11427.t2 MobiDBLite mobidb-lite consensus disorder prediction 514 543 -
19 g11427.t2 MobiDBLite mobidb-lite consensus disorder prediction 514 553 -
3 g11427.t2 PANTHER PTHR23322:SF56 FAS-ASSOCIATED FACTOR 1 7 630 4.1E-117
4 g11427.t2 PANTHER PTHR23322 FAS-ASSOCIATED PROTEIN 7 630 4.1E-117
2 g11427.t2 Pfam PF14555 UBA-like domain 8 41 7.2E-7
1 g11427.t2 Pfam PF00789 UBX domain 555 630 5.5E-12
20 g11427.t2 ProSiteProfiles PS50033 UBX domain profile. 551 628 17.446
17 g11427.t2 SMART SM00594 45neu3 314 459 1.8E-41
16 g11427.t2 SMART SM00166 ubx_3 547 630 2.5E-10
7 g11427.t2 SUPERFAMILY SSF54236 Ubiquitin-like 70 144 1.67E-8
8 g11427.t2 SUPERFAMILY SSF54236 Ubiquitin-like 169 245 5.54E-5
5 g11427.t2 SUPERFAMILY SSF52833 Thioredoxin-like 327 437 4.03E-5
6 g11427.t2 SUPERFAMILY SSF54236 Ubiquitin-like 519 630 3.21E-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

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