Gene loci information

Transcript annotation

  • This transcript has been annotated as Armadillo segment polarity protein.

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 g13374 g13374.t4 TSS g13374.t4 29585796 29585796
chr_1 g13374 g13374.t4 isoform g13374.t4 29585895 29588423
chr_1 g13374 g13374.t4 exon g13374.t4.exon1 29585895 29585898
chr_1 g13374 g13374.t4 exon g13374.t4.exon2 29586542 29586625
chr_1 g13374 g13374.t4 cds g13374.t4.CDS1 29586595 29586625
chr_1 g13374 g13374.t4 exon g13374.t4.exon3 29587360 29588423
chr_1 g13374 g13374.t4 cds g13374.t4.CDS2 29587360 29588423
chr_1 g13374 g13374.t4 TTS g13374.t4 NA NA

Sequences

>g13374.t4 Gene=g13374 Length=1152
AACGGTGTGAAAGGAGTAATTTGATCTCTGTCGCCCGTTAAATTTTCGCAACACACAATG
AGCTATCAAATGTCACAAAATCGCACGATGTCTCACAATCCTTATCAAAATTCCGAAATG
GCAATGGGAAAGGATCAACAAACGTTGATGTGGCAACAAAATTCATACTTGGCTGGCGGT
GATTCTGGCATTCAATCGGGTGCAATCACTCAAGTACCATCATTGAGCGGTAAAGATGAT
GATGAAATGGGAGGTGGTGATGATACACTTATGTTTGATCTTGATCAAGGTTTCAATCAA
AATTATACACAAGATCAAGTTGATGATATGAATCAGCAGTTAAATCAAACTCGTAGTCAA
CGAGTTCGTGCTGCAATGTTTCCAGAAACTTTGGAAGAAGGCATAGAAATTCCATCGACA
CAATTTGATCCACAACAACCAACTGCTGTTCAGCGGTTGTCTGAACCTTCACAAATGTTA
AAACACGCTGTTGTTAATTTGATTAATTATCAAGATGATGCAGATTTGGCCACACGTGCC
ATTCCTGAATTGATTAAATTACTTAATGATGAAGATCAAGTTGTTGTCTCACAAGCTGCA
ATGATGGTACATCAATTATCTAAGAAAGAAGCTTCACGTCATGCCATTATGAACAGTCCA
CAAATGGTTGCTGCTTTGGTTCGTGCATTGTCCACCAGCAATGACTTGGAAACAACAAAG
GGAGCTGTCGGAACCCTTCACAATTTATCACACCATCGTCAAGGTCTTTTGGCTATTTTC
AAAAGTGGTGGCATTCCTGCATTGGTCAAGTTGTTGTCATCACCAGTTGAAAGTGTTTTG
TTCTATGCAATCACAACATTACACAATCTTTTGCTTCATCAAGATGGTTCAAAAATGGCT
GTTCGTTTAGCTGGAGGCTTGCAAAAGATGGTCGCATTATTACAGCGCAATAACGTAAAG
TTCCTCGCCATCGTTACAGACTGCTTGCAAATTCTAGCTTATGGCAATCAAGAAAGCAAG
TTGATTATTTTAGCTTCCACTGGACCAATTGAGTTGGTTCGTATTATGCGTTCATATGAC
TATGAGAAGTTATTGTGGACAACATCACGTGTATTGAAAGTTCTATCAGTCTGCTCTAGT
AACAAACCAGCA

>g13374.t4 Gene=g13374 Length=365
MSYQMSQNRTMSHNPYQNSEMAMGKDQQTLMWQQNSYLAGGDSGIQSGAITQVPSLSGKD
DDEMGGGDDTLMFDLDQGFNQNYTQDQVDDMNQQLNQTRSQRVRAAMFPETLEEGIEIPS
TQFDPQQPTAVQRLSEPSQMLKHAVVNLINYQDDADLATRAIPELIKLLNDEDQVVVSQA
AMMVHQLSKKEASRHAIMNSPQMVAALVRALSTSNDLETTKGAVGTLHNLSHHRQGLLAI
FKSGGIPALVKLLSSPVESVLFYAITTLHNLLLHQDGSKMAVRLAGGLQKMVALLQRNNV
KFLAIVTDCLQILAYGNQESKLIILASTGPIELVRIMRSYDYEKLLWTTSRVLKVLSVCS
SNKPA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g13374.t4 Gene3D G3DSA:1.25.10.10 - 132 365 0.0000000
2 g13374.t4 PANTHER PTHR45976 ARMADILLO SEGMENT POLARITY PROTEIN 19 365 0.0000000
3 g13374.t4 PANTHER PTHR45976:SF4 CATENIN BETA-1 19 365 0.0000000
6 g13374.t4 PRINTS PR01869 Beta-catenin family signature 96 116 0.0000000
8 g13374.t4 PRINTS PR01869 Beta-catenin family signature 129 143 0.0000000
4 g13374.t4 PRINTS PR01869 Beta-catenin family signature 180 201 0.0000000
9 g13374.t4 PRINTS PR01869 Beta-catenin family signature 244 263 0.0000000
7 g13374.t4 PRINTS PR01869 Beta-catenin family signature 300 322 0.0000000
5 g13374.t4 PRINTS PR01869 Beta-catenin family signature 330 354 0.0000000
1 g13374.t4 Pfam PF00514 Armadillo/beta-catenin-like repeat 239 271 0.0000001
18 g13374.t4 ProSiteProfiles PS50176 Armadillo/plakoglobin ARM repeat profile. 160 200 11.2870000
17 g13374.t4 ProSiteProfiles PS50176 Armadillo/plakoglobin ARM repeat profile. 202 245 13.8770000
20 g13374.t4 ProSiteProfiles PS50176 Armadillo/plakoglobin ARM repeat profile. 244 286 14.7170000
19 g13374.t4 ProSiteProfiles PS50176 Armadillo/plakoglobin ARM repeat profile. 286 328 9.1520000
13 g13374.t4 SMART SM00185 arm_5 150 189 8.4000000
12 g13374.t4 SMART SM00185 arm_5 190 232 0.3100000
15 g13374.t4 SMART SM00185 arm_5 233 273 0.0000790
14 g13374.t4 SMART SM00185 arm_5 274 315 0.0460000
11 g13374.t4 SMART SM00185 arm_5 317 358 89.0000000
10 g13374.t4 SUPERFAMILY SSF48371 ARM repeat 144 364 0.0000000

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:0007155 cell adhesion BP
GO:0005515 protein binding MF
GO:0045296 cadherin binding 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