Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Transcription factor EB.

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 g2032 g2032.t1 TSS g2032.t1 14593983 14593983
chr_3 g2032 g2032.t1 isoform g2032.t1 14594646 14600986
chr_3 g2032 g2032.t1 exon g2032.t1.exon1 14594646 14595043
chr_3 g2032 g2032.t1 cds g2032.t1.CDS1 14594646 14595043
chr_3 g2032 g2032.t1 exon g2032.t1.exon2 14597215 14597410
chr_3 g2032 g2032.t1 cds g2032.t1.CDS2 14597215 14597410
chr_3 g2032 g2032.t1 exon g2032.t1.exon3 14597465 14597929
chr_3 g2032 g2032.t1 cds g2032.t1.CDS3 14597465 14597929
chr_3 g2032 g2032.t1 exon g2032.t1.exon4 14599812 14599965
chr_3 g2032 g2032.t1 cds g2032.t1.CDS4 14599812 14599965
chr_3 g2032 g2032.t1 exon g2032.t1.exon5 14600030 14600271
chr_3 g2032 g2032.t1 cds g2032.t1.CDS5 14600030 14600271
chr_3 g2032 g2032.t1 exon g2032.t1.exon6 14600339 14600464
chr_3 g2032 g2032.t1 cds g2032.t1.CDS6 14600339 14600464
chr_3 g2032 g2032.t1 exon g2032.t1.exon7 14600582 14600986
chr_3 g2032 g2032.t1 cds g2032.t1.CDS7 14600582 14600986
chr_3 g2032 g2032.t1 TTS g2032.t1 NA NA

Sequences

>g2032.t1 Gene=g2032 Length=1986
ATGAATGATAGCGGTTTCATCTCGGGTACTGAAATGAACGTTGACAATATTTTCTTTTAT
GATGAGGATAATTGTGTATCATCGCGCGAGAGAAGAATGCCTATAGTTTACAATAGAAGT
GAAAATAACAACAACAATAATAATAATATAATTGACGATCAATCAATGGGCACAGTTGAC
GATCAACAAAATACTTCATTGGATACTGTGCAGAAGCAAAAAAAGCACAAAGACTCAAAA
TATACACAAATTAAAGTAAATGTTGGAATTGATGAGGATCTTAAGATGCTACTTGACTTA
GACCCAAGTCTAATCGATGGTATCGATAATGGTGTGTTAGAAAAGGCCGTTGAACCAACA
CACAATGATTCGCGATTATTAGCGTTGCCACCGAAAATACCAACTTTTAAAACGATAACA
CCAACATCGCGCACTCAGTTAAAGACATTACTTCAGCGGGAGCAGTTGTTGCAAGAAGCA
GAACGTAAAGAGGCGGAAAGGAAGCGATTAGAACAAGAACAAGAAGAGCAGAAAGCAAAA
TTAGAGTCGCAAAAGGTCCCGCTTGAAGTTGATATTCCACCGCAAATCTTGCAAGTCTCG
ACTCGATTGGCAAATCCCACAAAATATCATGTGATACAAAAGCAAAAGAATCAAGTGAAA
CAATATCTAAGTGAATCATTCAAATCATCCGAGTCTTTGTACAATTTAATTCCATACCCG
GTTTTACAACATAGCAACAACAACAACGGCAACACAATGGCTGCGCTCGCGACCAAATCG
CAACCTGTGACAACATGTAATTCACCGAGTGTTAAGAACAACATAAATGCAAAATTACTT
AATCATACGGCAATCAAAAATGGCAATTTATTGAGTCAAAGTGCAAGTGAAATGGCTCAC
GTTCAAAGTACAGAATATTCGTCTGGGCAATCTAATGGCAGTTTTCCATTTGTGCTTCAA
CACCGATATATTGCGGCTGCTAGTCCATCCGAGGTCGCATCTTCTGCGATGTCACCAACA
ATTAGTTCAGTTGCAACCAGTGTGACAGATGCATCCGAGGCTGACGATTATATTGATGAA
ATATTAAACTACGAGTCAATAAAATGTGAAATGAATTCTGAATTAAAAATCAAACAAGAG
CCTCAGACACCACAAGGACTTTCACTTTCAGAAGCCGAAAAGGACAGGCAGAAGAAGGAC
AATCATAACATGATTGAGAGAAGGCGAAGATTTAACATAAATGATCGCATAAAGGAGCTC
GGTAGTTTGCTGCCAAAAAGCAATGAATCATATTACGAGATAGTGCGTGACGTTAGGCCG
AACAAAGGAACAATCCTTAAATCATCTGTTGACTACATCAAGTGCCTTAAGCAAGAAATT
AATCGATTAAGAAAGACTGAGTTGAAGCAAAAGGAGATGGAAATGCAAAATAGAAAGCTG
TTGATGAGAATACAGGAGCTTGAACAGCAAACAATAAATAACAATAACAACAACATACAA
TGTGGAAGTAGCGGATTTAGTTCATTGAATGCTATGTCAACAGCTCAACTACTCAATGAG
TATTCACCAGACACAAATCATCAAATCCCTGATGTCATAAGTAATGTTCAAACAATGAGC
CTCAATCATGCATCAGTAGTAGCGAAAAGTTATGTAGATGAAGACAGACTTTCAATAAAA
AATGAAGACTCGTTGTTCAATCATTCTGGCAGCAATAATAACAACTACGTGCAACAAAGT
AATCAAAATCACTTGCTCTATGAGACATTGCTCGCGAACAAACATCATCATAACCACCAT
CATCACCATCATCATCAGCATCATAATCAAGAGAACATCTCGACTGTTGATATTTCTGCA
ATTGAAATTGATCCGATTATTGTTAACTATGGATTAATGTCCATGCATCATGAGCCAAAT
ACTACTGTCGACAGTGGTCACGCCGATTCAGACTCACTCCTTAGTGATATTGATATGATT
GCATAG

>g2032.t1 Gene=g2032 Length=661
MNDSGFISGTEMNVDNIFFYDEDNCVSSRERRMPIVYNRSENNNNNNNNIIDDQSMGTVD
DQQNTSLDTVQKQKKHKDSKYTQIKVNVGIDEDLKMLLDLDPSLIDGIDNGVLEKAVEPT
HNDSRLLALPPKIPTFKTITPTSRTQLKTLLQREQLLQEAERKEAERKRLEQEQEEQKAK
LESQKVPLEVDIPPQILQVSTRLANPTKYHVIQKQKNQVKQYLSESFKSSESLYNLIPYP
VLQHSNNNNGNTMAALATKSQPVTTCNSPSVKNNINAKLLNHTAIKNGNLLSQSASEMAH
VQSTEYSSGQSNGSFPFVLQHRYIAAASPSEVASSAMSPTISSVATSVTDASEADDYIDE
ILNYESIKCEMNSELKIKQEPQTPQGLSLSEAEKDRQKKDNHNMIERRRRFNINDRIKEL
GSLLPKSNESYYEIVRDVRPNKGTILKSSVDYIKCLKQEINRLRKTELKQKEMEMQNRKL
LMRIQELEQQTINNNNNNIQCGSSGFSSLNAMSTAQLLNEYSPDTNHQIPDVISNVQTMS
LNHASVVAKSYVDEDRLSIKNEDSLFNHSGSNNNNYVQQSNQNHLLYETLLANKHHHNHH
HHHHHQHHNQENISTVDISAIEIDPIIVNYGLMSMHHEPNTTVDSGHADSDSLLSDIDMI
A

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2032.t1 CDD cd11397 bHLHzip_MITF_like 394 467 4.54611E-37
8 g2032.t1 Coils Coil Coil 148 183 -
7 g2032.t1 Coils Coil Coil 453 490 -
6 g2032.t1 Gene3D G3DSA:4.10.280.10 HLH 407 494 2.7E-24
12 g2032.t1 MobiDBLite mobidb-lite consensus disorder prediction 162 182 -
11 g2032.t1 MobiDBLite mobidb-lite consensus disorder prediction 376 390 -
13 g2032.t1 MobiDBLite mobidb-lite consensus disorder prediction 376 402 -
3 g2032.t1 PANTHER PTHR45776 MIP04163P 134 652 6.3E-79
4 g2032.t1 PANTHER PTHR45776:SF2 MIP04163P 134 652 6.3E-79
2 g2032.t1 Pfam PF15951 MITF/TFEB/TFEC/TFE3 N-terminus 144 275 1.8E-16
1 g2032.t1 Pfam PF00010 Helix-loop-helix DNA-binding domain 398 456 4.0E-14
14 g2032.t1 ProSiteProfiles PS50888 Myc-type, basic helix-loop-helix (bHLH) domain profile. 397 456 16.05
10 g2032.t1 SMART SM00353 finulus 403 462 1.2E-11
5 g2032.t1 SUPERFAMILY SSF47459 HLH, helix-loop-helix DNA-binding domain 392 464 4.58E-15

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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific MF
GO:0046983 protein dimerization activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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