Gene loci information

Transcript annotation

  • This transcript has been annotated as Phospholipase D1.

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 g3603 g3603.t4 isoform g3603.t4 26673606 26674753
chr_3 g3603 g3603.t4 exon g3603.t4.exon1 26673606 26674157
chr_3 g3603 g3603.t4 cds g3603.t4.CDS1 26673606 26674157
chr_3 g3603 g3603.t4 exon g3603.t4.exon2 26674222 26674753
chr_3 g3603 g3603.t4 cds g3603.t4.CDS2 26674222 26674587
chr_3 g3603 g3603.t4 TSS g3603.t4 NA NA
chr_3 g3603 g3603.t4 TTS g3603.t4 NA NA

Sequences

>g3603.t4 Gene=g3603 Length=1084
GGGTTGCTGTATAAGATGTAATTATTTCTGTTCTGAAAGCTGCTGCAGTAGTTGGCAAGG
ACGGTGGCTTTTTGTGAAAGAAACTTTTTTTGGATTGGTTCGTCCGAAAGATGGAACTAT
TCGAAGTATAATATTATTTGATCAAGGCTTTGAGACGTCTCTTGGTATGTATAGTACAGG
GTTACGAACTGGCCTTCAAATTGCCACAAATTCACGCTATATTGTACTGAAATTTCCAAC
AAAAAAATTAGCAAAAGAGTGGAACAATTATTTCAAACAAATTGCTAATTCTACTGCACG
TGATTTTACATCACCAAATCCACATCAATCGTTTGCACCAGTTCGTACATCAACTCTAGC
GTCGTGGTTTGTTGATGGGTCAAATTATATGAGTGCAGTGGCAGATGCTCTTGAAGGTGC
ACTCGAAGAGATTTTTATTGCCGATTGGTGGTTAAGTCCAGAAATTTATATGAAACGCCC
AACACTTGATGGAGAATATTGGCGCTTGGATAAAATTTTATTGAGAAAAGCTCGTCAAGG
TGTAAAAATATTTGTTCTACTTTACAAAGAAGTTGAAATGGCTCTTGGTTTGAATAGCTA
TTACAGCAAACAGAGACTTGTTCAGTTGCATGAAAATATTAAAGTTTTACGTCATCCTGA
TCATGTTAGAGTTGGTGTTTTCTTTTGGGCTCATCATGAGAAACTTGTTGTTATTGACCA
AACTTATGCATTTGTTGGTGGCATAGATTTAGCTTATGGAAGATGGGATGATCATAAACA
TCGACTTACAGACATGGGAAGTATTAGTATTTCAACAAAGACAACAAGTCGACGATCTTT
TGTGATGATTGAGAATCCATTACGCTCTCTAATTGTTCAATCAACTGAAATCGTACAAGC
AACTACTACGACAAGATCTGAAAATCAAAATATGAAATCAGAAGCGATCACTGATTCAAT
GGCAAATGGCGATAAGAGAGAAAATGAACCAATAGGGCAGGAAATTGATGAACACATTAA
AAAGAACACTCCGGAAATGAAACGTAAGGGTATTACTGAAAAAATTAAAGACAATATGAA
AAAT

>g3603.t4 Gene=g3603 Length=306
MYSTGLRTGLQIATNSRYIVLKFPTKKLAKEWNNYFKQIANSTARDFTSPNPHQSFAPVR
TSTLASWFVDGSNYMSAVADALEGALEEIFIADWWLSPEIYMKRPTLDGEYWRLDKILLR
KARQGVKIFVLLYKEVEMALGLNSYYSKQRLVQLHENIKVLRHPDHVRVGVFFWAHHEKL
VVIDQTYAFVGGIDLAYGRWDDHKHRLTDMGSISISTKTTSRRSFVMIENPLRSLIVQST
EIVQATTTTRSENQNMKSEAITDSMANGDKRENEPIGQEIDEHIKKNTPEMKRKGITEKI
KDNMKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g3603.t4 CDD cd09138 PLDc_vPLD1_2_yPLD_like_1 65 210 6.16308E-98
5 g3603.t4 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A 58 215 6.9E-17
8 g3603.t4 MobiDBLite mobidb-lite consensus disorder prediction 248 306 -
9 g3603.t4 MobiDBLite mobidb-lite consensus disorder prediction 248 262 -
10 g3603.t4 MobiDBLite mobidb-lite consensus disorder prediction 264 306 -
2 g3603.t4 PANTHER PTHR18896:SF57 PHOSPHOLIPASE D1 4 238 1.3E-94
3 g3603.t4 PANTHER PTHR18896 PHOSPHOLIPASE D 4 238 1.3E-94
1 g3603.t4 Pfam PF00614 Phospholipase D Active site motif 173 199 1.7E-8
11 g3603.t4 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile. 172 199 13.238
7 g3603.t4 SMART SM00155 pld_4 172 199 5.9E-6
4 g3603.t4 SUPERFAMILY SSF56024 Phospholipase D/nuclease 47 204 5.65E-31

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:0003824 catalytic 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