Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein similar.

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 g1184 g1184.t1 TTS g1184.t1 8552572 8552572
chr_3 g1184 g1184.t1 isoform g1184.t1 8552624 8587593
chr_3 g1184 g1184.t1 exon g1184.t1.exon1 8552624 8552953
chr_3 g1184 g1184.t1 cds g1184.t1.CDS1 8552624 8552953
chr_3 g1184 g1184.t1 exon g1184.t1.exon2 8559519 8559919
chr_3 g1184 g1184.t1 cds g1184.t1.CDS2 8559519 8559919
chr_3 g1184 g1184.t1 exon g1184.t1.exon3 8559985 8560510
chr_3 g1184 g1184.t1 cds g1184.t1.CDS3 8559985 8560510
chr_3 g1184 g1184.t1 exon g1184.t1.exon4 8562668 8562939
chr_3 g1184 g1184.t1 cds g1184.t1.CDS4 8562668 8562939
chr_3 g1184 g1184.t1 exon g1184.t1.exon5 8565164 8565819
chr_3 g1184 g1184.t1 cds g1184.t1.CDS5 8565164 8565819
chr_3 g1184 g1184.t1 exon g1184.t1.exon6 8580163 8580304
chr_3 g1184 g1184.t1 cds g1184.t1.CDS6 8580163 8580304
chr_3 g1184 g1184.t1 exon g1184.t1.exon7 8582927 8583033
chr_3 g1184 g1184.t1 cds g1184.t1.CDS7 8582927 8583033
chr_3 g1184 g1184.t1 exon g1184.t1.exon8 8583097 8583266
chr_3 g1184 g1184.t1 cds g1184.t1.CDS8 8583097 8583266
chr_3 g1184 g1184.t1 exon g1184.t1.exon9 8583332 8583553
chr_3 g1184 g1184.t1 cds g1184.t1.CDS9 8583332 8583553
chr_3 g1184 g1184.t1 exon g1184.t1.exon10 8583625 8583845
chr_3 g1184 g1184.t1 cds g1184.t1.CDS10 8583625 8583845
chr_3 g1184 g1184.t1 exon g1184.t1.exon11 8583920 8584107
chr_3 g1184 g1184.t1 cds g1184.t1.CDS11 8583920 8584107
chr_3 g1184 g1184.t1 exon g1184.t1.exon12 8587088 8587593
chr_3 g1184 g1184.t1 cds g1184.t1.CDS12 8587088 8587593
chr_3 g1184 g1184.t1 TSS g1184.t1 NA NA

Sequences

>g1184.t1 Gene=g1184 Length=3741
ATGAATAACAATTATTATTATCCATATGATGATAATGCAAATTTTAATTATGGTTGCGAT
AATTCAAACCAATTTAATTATTACAATAGTAATAATAATGGTCAAGTGTCCAATTTTCAT
CAATATCCGATGCAACAGCAGCAAAGTTTTACCAATTCAAATTATTCATATAATAATAGT
TGCAATAATTATGATGACAGTGTAGTGCCTACAAATTTCTATGAAAATACATCTGTCAAT
GATTATCTAATGCAAGTGCAACAACCAAATTATAATAATTACTATACTAATATGAGTCAA
AGTTCGCATTACAATTCAAACGGTTATGTTGATCAATCTGTAGCTGTTGGAAATGCTTCT
AATTATGTCTTTAATGAATCATATCAAACTCATCCACCATGTCAAGGTCCACAGCCGTGG
AATTATGCTCATTGTTATGGCTATTTTGGTGACGAACCATGCCAATTTTCTAACTTTACT
AGTGTTATAGATATGGAAGATTTTATGAACAATGAAAAACGCAAAGAAAAGTCTCGCGAT
GCAGCAAGATGCCGTCGTTCGAGAGAAACAGAGATATTTACGGAACTTGCAAATTCACTT
CCAATAAAACAAGATGAAATTGATCATCTTGACAAAGCTTCTGTTATGCGTCTTTCCATT
TCTTATCTCAAGATTCGTAATATGCTTGAGTTGTTTCCAAAAATTAAAAATTTGGATATT
CCCGTTGCTGAGCTCGAAAATGGTGATGAAACAGATGAGGATGTTAAGGATGTCAAGATT
GACGTTTTGAGAAAAATTGTTGAGGATGAGAAATTTGCTCTAAAAGCACTCGATGGATTC
TTGCTTGTGCTCAATGCTGAAGGCGATATTACATATGTATCGCAAAACATTGCAGAATAC
CTGGGTCTAGCAAAAATTGATTTATTGGGTCAACCGATATGGGACTACACACATGCGTGT
GATCACGATGAACTTCGTGAAGCTCTTAATGGCCGCAAAACTTCACCGTCTGAAGTTGTT
AATGGCGCAAAATCAGCTGATTGTAATCCATTATTACATCGTGATATGATGATTCGTTTG
AAATGCACACTTACAAAGAGTGGACGTTTTGTTAACATCAAAAGTGCTTCTTATAAGGTG
ATTCATTTGACGGGTCATATTGTGTTCAAAGATGATGGCTATCGTCAATTGTTGGCAATT
GGTCGGCCACTAGCTCATCCATCAAATATCGAGGTGCCTTTGGGTTCCAGCACTTTTCTT
ACAAAACATACATTAGATATGAAATTCAGCTTTGTCGATAGTCCAAAAATGTTTGAGCTG
ATGGGGTACAAACCTGAACATTTGTTGGGCAAATCGCTTTATGAATATCATCATGGTAGC
GATTCGGAGAGTCTCATGTCAAGTTTCAAGTGCCTAATCAGCAAAGGTCAAACTGAAACT
AACCGCTACCGATTTTTGGCACGTAATGGTGGTTACGTTTGGATCGTAACTCAAGCAACT
GTAGTGTTCGAGAAACAGAAGCCCCAAAGTGTCGTCTGCGTTAGTTACGTTGTGAGTGGA
ATAGAAAATGAACATGAAATTTATTCATGTGCTCAACTCGAGGCACAACAGCAAGAATTG
TCAAAAGCAATTGAGACAACAACAGCAGTAGTTGAGACACAAAGTGACATAAAAGTGATT
AAAAAGGACAATATTGTGCTCGGTATAAGTGATTTGAAACAACAGCAACAGAAAAAATTA
TCAACTGCCGAAGCAAAAGGCATTAGTGGAACAATTACTAATAATAATATTAAAAGTGCT
GCCAATAATAAACCATTAACGATTGCTGACAAAAAGGAAAACAATAGCGATAACAAGAAC
ACAAGTGTTGGACAATCATTGGTTACAATCAATCCAATAAATACTATTAAAGTTAATAAC
TGTGAAATTATAAATCGTCGTCCACACTCAGTTACGGCTGCAATTTTCGCACAGTCGACA
GTTTTAAAATCACAAGCAATAGCTACATCTAATGCTATAATAGCATCTGCTGCTCAAATA
TCCAGGAAAACTAAAAAACAAACAGCAACAGCAGGAATAAAAGTATTTCGTCCAACACAG
CAAGTAGTAGCAAACGCCGCTACAAGCGTTACATCAACAATTTTTGCACCACGTACGAAG
GATATGAATAAAGGATACTTGATGTTCGCAGAAGACGACACAGGACTAACAATGCTGAAA
GATGAGCCGGATGATTTAACACATTTGGCACCAACTGCCGGCGACGCATGCATCTCGCTT
GATGAATCTGCTCCTTTCTTTGATATGTTTGATGACTTCATGATACCCGATAATTATAAT
ACATTGTTAACAGACGATTTGGACAGTCAATGCAGTAAAACAACAACAACGAGTAGTTCT
AGTAATGATCCATTTATTAACTATAGAGATGAGTCAAGTGATGTTAGCAATTCTCCTCAC
TTGCTTTCACCGGGTTTGTCAAAGAGTCCTGGTGCAAATAGTAGTATACCGTCTTTATGC
AGTCCTGGCTCTCTACCAGAAGATGAGCTTGCATTTATGACATTAAATATGGATGATGAT
TTGGATATGTCTATGCGTGCCCCTTATATTTCAATGAGCGAATCAGCTGAGCTTCCATTA
CTAATCGCAGAAGATCTTATGTGGGGTGCTGCACCTGACATAAAACAATCGCTAACAATT
AATAGAAAAATGGAAATTCCAATTAATGTAGAGCAAGAACAGCAAATAAGCCAACAACAA
CATACTGAAAGTCCTAACAAACAGCAGCAACAACAAATTACAACGCAAAATGTACTTGCA
AAGAATGCAATGGATTCGAGTTTAGCATCATTGCTTTGTAGCCAATTATTGCAGCAACAG
CTACTAAATCAGCAACAAACAGAACAACAAATTATCCTAAGTAAAAATCCAGAAATTAAA
ATCAAAATTTTGGATAACTTAATTGATGCGACTAACGAGCTTGATCACAACACCACCAAC
ACTAAAAGCGCTTCAAATGTTGAATGCACGATGAACGATCTATTTCAATTAAAGAAACAA
CAACCAATTACTAAACAAGAAAGCAAGGAACATACGATTGTTAATCAATTGCAATCTGAA
TTGGAAAATAGTTCACGAGTGAAAACAACAGTAAATCAACATAAACGTCCATCAATATCG
TGTGAAATTAGTTCGAAACGGATTAAAGCACAGGAAACAATCAAAGCAACACCTCAATTG
CTTCAGCAACTGATAACGGCGACTGGAGTGAGTCCAAAAGGGCGCCAGAAAATTCAACTC
AATCATAATAACGATGAAAATCAGCGATGGAAACCACAACAGCAACAACAAACACAACAA
CAACCGGCATCGAATTCTGTATTAATGAATCTGCTAGTGAGTGGATGTGATGAGCCACTT
TCAATTGATCCACCAGAAGATTTACTTGAGAATGCTGAAAGTATGACATCACCTATTGTC
ATTAATGACAAGATGTTATCTCATTCTGCTGTAATGATTGCACCGAATGTTAATCACAAC
ACTGCACATCATCATCTATCATCAAATGGAATGGAAATTTATCAAACAGTTCCCAATGGA
AATGGACGAAATGTCGGCACATCAGGTGATGCATATAACAACTTTATTGATTCTGATGCC
ATAACATCGATTCTCATGGACTTGAATGAGCAAGATTATGAATGTAATATCGCGGTCAAT
GATATCTTGAAATTGATGTAA

>g1184.t1 Gene=g1184 Length=1246
MNNNYYYPYDDNANFNYGCDNSNQFNYYNSNNNGQVSNFHQYPMQQQQSFTNSNYSYNNS
CNNYDDSVVPTNFYENTSVNDYLMQVQQPNYNNYYTNMSQSSHYNSNGYVDQSVAVGNAS
NYVFNESYQTHPPCQGPQPWNYAHCYGYFGDEPCQFSNFTSVIDMEDFMNNEKRKEKSRD
AARCRRSRETEIFTELANSLPIKQDEIDHLDKASVMRLSISYLKIRNMLELFPKIKNLDI
PVAELENGDETDEDVKDVKIDVLRKIVEDEKFALKALDGFLLVLNAEGDITYVSQNIAEY
LGLAKIDLLGQPIWDYTHACDHDELREALNGRKTSPSEVVNGAKSADCNPLLHRDMMIRL
KCTLTKSGRFVNIKSASYKVIHLTGHIVFKDDGYRQLLAIGRPLAHPSNIEVPLGSSTFL
TKHTLDMKFSFVDSPKMFELMGYKPEHLLGKSLYEYHHGSDSESLMSSFKCLISKGQTET
NRYRFLARNGGYVWIVTQATVVFEKQKPQSVVCVSYVVSGIENEHEIYSCAQLEAQQQEL
SKAIETTTAVVETQSDIKVIKKDNIVLGISDLKQQQQKKLSTAEAKGISGTITNNNIKSA
ANNKPLTIADKKENNSDNKNTSVGQSLVTINPINTIKVNNCEIINRRPHSVTAAIFAQST
VLKSQAIATSNAIIASAAQISRKTKKQTATAGIKVFRPTQQVVANAATSVTSTIFAPRTK
DMNKGYLMFAEDDTGLTMLKDEPDDLTHLAPTAGDACISLDESAPFFDMFDDFMIPDNYN
TLLTDDLDSQCSKTTTTSSSSNDPFINYRDESSDVSNSPHLLSPGLSKSPGANSSIPSLC
SPGSLPEDELAFMTLNMDDDLDMSMRAPYISMSESAELPLLIAEDLMWGAAPDIKQSLTI
NRKMEIPINVEQEQQISQQQHTESPNKQQQQQITTQNVLAKNAMDSSLASLLCSQLLQQQ
LLNQQQTEQQIILSKNPEIKIKILDNLIDATNELDHNTTNTKSASNVECTMNDLFQLKKQ
QPITKQESKEHTIVNQLQSELENSSRVKTTVNQHKRPSISCEISSKRIKAQETIKATPQL
LQQLITATGVSPKGRQKIQLNHNNDENQRWKPQQQQQTQQQPASNSVLMNLLVSGCDEPL
SIDPPEDLLENAESMTSPIVINDKMLSHSAVMIAPNVNHNTAHHHLSSNGMEIYQTVPNG
NGRNVGTSGDAYNNFIDSDAITSILMDLNEQDYECNIAVNDILKLM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g1184.t1 CDD cd11433 bHLH-PAS_HIF 174 230 8.56542E-30
12 g1184.t1 CDD cd00130 PAS 277 329 3.70949E-11
11 g1184.t1 CDD cd00130 PAS 416 504 5.37967E-13
8 g1184.t1 Gene3D G3DSA:3.30.450.20 - 265 404 1.8E-28
9 g1184.t1 Gene3D G3DSA:3.30.450.20 - 415 586 3.9E-30
17 g1184.t1 MobiDBLite mobidb-lite consensus disorder prediction 913 934 -
3 g1184.t1 PANTHER PTHR23043 HYPOXIA-INDUCIBLE FACTOR 1 ALPHA 164 682 2.0E-172
4 g1184.t1 PANTHER PTHR23043:SF17 PROTEIN SIMILAR 164 682 2.0E-172
1 g1184.t1 Pfam PF00989 PAS fold 273 330 1.0E-6
2 g1184.t1 Pfam PF08447 PAS fold 434 514 2.9E-14
19 g1184.t1 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 173 226 12.157
20 g1184.t1 ProSiteProfiles PS50112 PAS repeat profile. 273 330 14.159
21 g1184.t1 ProSiteProfiles PS50112 PAS repeat profile. 434 476 11.359
13 g1184.t1 SMART SM00353 finulus 179 231 5.5E-4
14 g1184.t1 SMART SM00091 pas_2 268 334 4.2E-11
15 g1184.t1 SMART SM00091 pas_2 407 474 0.016
16 g1184.t1 SMART SM00086 pac_2 480 521 4.3E-4
7 g1184.t1 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 171 225 3.97E-5
6 g1184.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 277 331 9.16E-12
5 g1184.t1 SUPERFAMILY SSF55785 PYP-like sensor domain (PAS domain) 419 519 3.14E-19
18 g1184.t1 TIGRFAM TIGR00229 sensory_box: PAS domain S-box protein 434 513 1.7E-6

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
GO:0006355 regulation of transcription, DNA-templated BP
GO:0046983 protein dimerization 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