Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein scalloped.

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 g13836 g13836.t2 TTS g13836.t2 32642302 32642302
chr_1 g13836 g13836.t2 isoform g13836.t2 32642652 32679393
chr_1 g13836 g13836.t2 exon g13836.t2.exon1 32642652 32642765
chr_1 g13836 g13836.t2 cds g13836.t2.CDS1 32642652 32642765
chr_1 g13836 g13836.t2 exon g13836.t2.exon2 32642836 32643070
chr_1 g13836 g13836.t2 cds g13836.t2.CDS2 32642836 32643070
chr_1 g13836 g13836.t2 exon g13836.t2.exon3 32643135 32643358
chr_1 g13836 g13836.t2 cds g13836.t2.CDS3 32643135 32643358
chr_1 g13836 g13836.t2 exon g13836.t2.exon4 32643428 32643643
chr_1 g13836 g13836.t2 cds g13836.t2.CDS4 32643428 32643643
chr_1 g13836 g13836.t2 exon g13836.t2.exon5 32647245 32647375
chr_1 g13836 g13836.t2 cds g13836.t2.CDS5 32647245 32647375
chr_1 g13836 g13836.t2 exon g13836.t2.exon6 32666785 32666923
chr_1 g13836 g13836.t2 cds g13836.t2.CDS6 32666785 32666923
chr_1 g13836 g13836.t2 exon g13836.t2.exon7 32666984 32667108
chr_1 g13836 g13836.t2 cds g13836.t2.CDS7 32666984 32667108
chr_1 g13836 g13836.t2 exon g13836.t2.exon8 32679378 32679393
chr_1 g13836 g13836.t2 cds g13836.t2.CDS8 32679378 32679393
chr_1 g13836 g13836.t2 TSS g13836.t2 NA NA

Sequences

>g13836.t2 Gene=g13836 Length=1200
ATGCTAATTTTTGGAGACGGCGGACTTGGAGCCGGCACAATAACGTCCAGGTGGCCTCCA
GTTGCTGGCCCAGGGCCAGAAAACGGCACCGGTGTGGATGGAAAACATCTTGATGTCGGC
GATATGAGTGATGTCAGTGATGACGAAAAGGACTTGTCGTCGGCAGATGCCGAAGGCGTT
TGGAGTCCTGACATCGAGCAAAGCTTCCAAGAAGCCCTCGCCATTTATCCACCATGTGGT
CGACGAAAAATTATACTATCAGAAGAGGGAAAGATGTATGGACGAAATGAGTTAATAGCG
CGCTACATTAAGCTCAGAACTGGTAAAACGAGAACGCGAAAGCAAGTCAGCTCACATATA
CAAGTCTTAGCTAGAAGAAAATTACGCGAATTTCAAGCAAAAATGAAGGTGCAATTTTGG
CAACCGGGATTACAACCAAGCACCTCTCAAGATGTAAAACCATTCACACAACCCGCTTAT
CCTGGTGGCAAGACAGCAACAGCCGTAGCAATTGATGGAACCTTACAGACACAGCACTCC
GAAGGTAGAAGTATTGCTACACAAAAGTTCAGACTCGTCGAATTCTCTGCATATCTTGAT
CTAAATACCGATGAAACTGTAAGTGATTATCACAAGCATCTCTTTGTACATATAGCCGAT
CAGCCAACGCATCCACTCCTCGAGTCAGTCGACGTGAAAGAAATCTACGACAAATTTCCA
CAGAAAAGTGGTGGTTTAAAAGAGCTATATGAAAAAGGTCCGCAGAATGCCTTCTTCTTG
GTAAAATTCTGGGCCGATCTCAATACAAATATTCAAAACGATACTGGTGCATTTTATGGT
GTCAGCAGTCACTTCGAAAGTAGTGAGAATGTAGTCATCACATGTTCCACAAAAGTGTGT
TCCTTCGGCAAGCAGGTGGTTGAAAAAGTCGAAACGGAATATTCACGATTCGAAAATGGA
CGCTATGTGTATCGTATACATCGGTCGCCAATGTGCGATTATATGATAAATTTCATCAAT
AAACTTAAACGACTGCCCGAGAAATATATGATGAACAGTGTCTTAGAAAACTTTACCATT
CTTCAGGTAATATCAAATAAAGAGACACAAGAGACCCTATTGTGCATCGCGTTTGTATTT
GAAGTTTCAACATCTGAACATGGTGCACAACATCACATTTATAGATTGATAAAAGATTAG

>g13836.t2 Gene=g13836 Length=399
MLIFGDGGLGAGTITSRWPPVAGPGPENGTGVDGKHLDVGDMSDVSDDEKDLSSADAEGV
WSPDIEQSFQEALAIYPPCGRRKIILSEEGKMYGRNELIARYIKLRTGKTRTRKQVSSHI
QVLARRKLREFQAKMKVQFWQPGLQPSTSQDVKPFTQPAYPGGKTATAVAIDGTLQTQHS
EGRSIATQKFRLVEFSAYLDLNTDETVSDYHKHLFVHIADQPTHPLLESVDVKEIYDKFP
QKSGGLKELYEKGPQNAFFLVKFWADLNTNIQNDTGAFYGVSSHFESSENVVITCSTKVC
SFGKQVVEKVETEYSRFENGRYVYRIHRSPMCDYMINFINKLKRLPEKYMMNSVLENFTI
LQVISNKETQETLLCIAFVFEVSTSEHGAQHHIYRLIKD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g13836.t2 Gene3D G3DSA:1.10.10.1610 - 54 134 3.0E-39
10 g13836.t2 Gene3D G3DSA:2.70.50.80 - 181 399 1.3E-111
4 g13836.t2 PANTHER PTHR11834 TRANSCRIPTIONAL ENHANCER FACTOR TEF RELATED 38 140 3.4E-186
6 g13836.t2 PANTHER PTHR11834:SF4 TRANSCRIPTIONAL ENHANCER FACTOR TEF-1 38 140 3.4E-186
3 g13836.t2 PANTHER PTHR11834 TRANSCRIPTIONAL ENHANCER FACTOR TEF RELATED 138 399 3.4E-186
5 g13836.t2 PANTHER PTHR11834:SF4 TRANSCRIPTIONAL ENHANCER FACTOR TEF-1 138 399 3.4E-186
13 g13836.t2 PIRSF PIRSF002603 TEF 6 152 4.8E-65
12 g13836.t2 PIRSF PIRSF002603 TEF 137 399 5.1E-128
9 g13836.t2 PRINTS PR00065 TEA domain signature 61 75 1.5E-22
8 g13836.t2 PRINTS PR00065 TEA domain signature 94 108 1.5E-22
7 g13836.t2 PRINTS PR00065 TEA domain signature 109 123 1.5E-22
1 g13836.t2 Pfam PF01285 TEA/ATTS domain 58 123 8.9E-27
2 g13836.t2 Pfam PF17725 YAP binding domain 189 396 3.9E-80
14 g13836.t2 ProSitePatterns PS00554 TEA domain signature. 94 122 -
16 g13836.t2 ProSiteProfiles PS51088 TEA domain profile. 54 130 30.006
15 g13836.t2 SMART SM00426 tea2 53 123 8.8E-51

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:0035329 hippo signaling BP
GO:0006355 regulation of transcription, DNA-templated BP
GO:0003700 DNA-binding transcription factor 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