Gene loci information

Transcript annotation

  • This transcript has been annotated as Embryonic polarity protein dorsal.

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_2 g6007 g6007.t2 isoform g6007.t2 13470576 13483139
chr_2 g6007 g6007.t2 exon g6007.t2.exon1 13470576 13470808
chr_2 g6007 g6007.t2 cds g6007.t2.CDS1 13470576 13470808
chr_2 g6007 g6007.t2 exon g6007.t2.exon2 13470928 13471106
chr_2 g6007 g6007.t2 cds g6007.t2.CDS2 13470928 13471106
chr_2 g6007 g6007.t2 exon g6007.t2.exon3 13471196 13471523
chr_2 g6007 g6007.t2 cds g6007.t2.CDS3 13471196 13471497
chr_2 g6007 g6007.t2 exon g6007.t2.exon4 13473778 13473822
chr_2 g6007 g6007.t2 exon g6007.t2.exon5 13482919 13483139
chr_2 g6007 g6007.t2 TSS g6007.t2 13483263 13483263
chr_2 g6007 g6007.t2 TTS g6007.t2 NA NA

Sequences

>g6007.t2 Gene=g6007 Length=1006
TCTAAAAGTGAAGTGCAAAATTTAGCAATTTTAAACAACTAGAAACATCGTGTTATCAAA
AAAAACATTTGTGTTCAGTTCTGATAAGATAGCAGAGTGAAAAAAAATTTAAACCATTGC
CGCAATTTTTTTTGGGACAATTTACAAGTTTTTGTGTGTTTTCAAATAAAAGTTTAAAAA
AAATTTCAAACACCGACCTTCAACAACAAAATCAAAATCAACAGTTGACGAGGTTTCAGA
CTTATCGATTCACATAAGTGATGTCATTGCAGTAATTGAAAGTACAGATCCAATGTTTCC
AATTGATTTAAATTCAATGGCACCTGTAGTAAACGGAAATATGCAAACAAATATGGCACC
ACAACAGCAACAACAACAATCACCACAAGAAGCAATACCTTATGTCGCAATATTAGAGCA
ACCAGCATCAAAAGCACTTCGTTTTCGCTATGAATGCGAAGGTAGAAGTGCAGGATCAAT
TCCTGGAGCAAATAGCACAGCAGATAATAAAACATACCCAACAATACAGATCAAAAATTA
TGTTGGAAAAGCAGTTGTAGTTGTATCATGCGTTACCAAAGATTTTCCCTACAAACCCCA
TCCACATAATTTGGTCGGAAAAGAAGGTTGCAAGAAGGGTGTGTGCACATTGGAAATCAA
TTCTGATGACATGAAAATGGTCTTTAGTAATTTGGGCATTCAATGTGTTAAACGTCGCGA
TATTGAAGAAGCTTTAAGAATTCGTGAAGAAATTCGTGTTGATCCGTACAGAACTGGTTA
CACACATCGCAATCAGCCATCGAGTATTGATTTGAATGCAGTTCGTTTATGCTTTCAAGT
ATTTTTGGAAGGTCCACAAAGAGGCAGATTCACACAACCACTGAAACCAGTCGTGTCAGA
ACCGATTTTCGATAAAAAGTCAATGTCAGATTTGGTGATAACAAAATTGAGCCATTGTAA
TGCTTTCTGCAATGGTGGACAGGAAATAATATTATTATGTGAAAAG

>g6007.t2 Gene=g6007 Length=238
MFPIDLNSMAPVVNGNMQTNMAPQQQQQQSPQEAIPYVAILEQPASKALRFRYECEGRSA
GSIPGANSTADNKTYPTIQIKNYVGKAVVVVSCVTKDFPYKPHPHNLVGKEGCKKGVCTL
EINSDDMKMVFSNLGIQCVKRRDIEEALRIREEIRVDPYRTGYTHRNQPSSIDLNAVRLC
FQVFLEGPQRGRFTQPLKPVVSEPIFDKKSMSDLVITKLSHCNAFCNGGQEIILLCEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g6007.t2 CDD cd07887 RHD-n_Dorsal_Dif 36 209 3.0588E-108
8 g6007.t2 Gene3D G3DSA:2.60.40.340 - 36 206 5.2E-72
7 g6007.t2 Gene3D G3DSA:2.60.40.10 Immunoglobulins 207 238 5.0E-7
2 g6007.t2 PANTHER PTHR24169 NUCLEAR FACTOR NF-KAPPA-B PROTEIN 18 238 1.2E-82
5 g6007.t2 PRINTS PR00057 Transcription factor NF-KB signature 42 59 2.2E-16
4 g6007.t2 PRINTS PR00057 Transcription factor NF-KB signature 197 211 2.2E-16
3 g6007.t2 PRINTS PR00057 Transcription factor NF-KB signature 228 238 2.2E-16
1 g6007.t2 Pfam PF00554 Rel homology DNA-binding domain 38 208 2.5E-69
10 g6007.t2 ProSitePatterns PS01204 NF-kappa-B/Rel/dorsal domain signature. 51 57 -
11 g6007.t2 ProSiteProfiles PS50254 NF-kappa-B/Rel/dorsal domain profile. 33 212 76.35
6 g6007.t2 SUPERFAMILY SSF49417 p53-like transcription factors 36 216 4.04E-73

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:0003677 DNA binding MF
GO:0006355 regulation of transcription, DNA-templated BP
GO:0005737 cytoplasm CC
GO:0003700 DNA-binding transcription factor 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