Gene loci information

Transcript annotation

  • This transcript has been annotated as 5’-3’ exonuclease PLD3.

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 g13640 g13640.t1 TSS g13640.t1 31390225 31390225
chr_1 g13640 g13640.t1 isoform g13640.t1 31390318 31392773
chr_1 g13640 g13640.t1 exon g13640.t1.exon1 31390318 31390368
chr_1 g13640 g13640.t1 cds g13640.t1.CDS1 31390318 31390368
chr_1 g13640 g13640.t1 exon g13640.t1.exon2 31390909 31391183
chr_1 g13640 g13640.t1 cds g13640.t1.CDS2 31390909 31391183
chr_1 g13640 g13640.t1 exon g13640.t1.exon3 31391428 31392210
chr_1 g13640 g13640.t1 cds g13640.t1.CDS3 31391428 31392210
chr_1 g13640 g13640.t1 exon g13640.t1.exon4 31392269 31392434
chr_1 g13640 g13640.t1 cds g13640.t1.CDS4 31392269 31392434
chr_1 g13640 g13640.t1 exon g13640.t1.exon5 31392495 31392773
chr_1 g13640 g13640.t1 cds g13640.t1.CDS5 31392495 31392773
chr_1 g13640 g13640.t1 TTS g13640.t1 31393035 31393035

Sequences

>g13640.t1 Gene=g13640 Length=1554
ATGAAAATTTTTGCGGTTAATACTGAAGTTGAAAAGGATTTAAAAAAGCTAACAGTACTC
GAGTCAAATAATCGCGATCTCAATCAAGTTCCTGTTGGTGACGATGATTTTGAACTGTGG
GATTATTCACAAATGTTGAGGAATCAGCAACGATATAAGTGGAATAATAATGGAATGGTT
TGCAAGCCTTCCTGCATTCCTATTTTTTTCATCCTCATTCTTATCGTTCTCGTTGTGCTT
CTTCCACTTCTCGATTCGCATAACGATAACAAAGTGTTGGGTCGAAATGGTACAATAATT
GGTTGGAATTGTGTAGATGAATGCAGCATTCAACTGGTCGAATCAATTCCAGAAGGTTTA
GTTTATGATCCTGACAGTCCATCATTTATGTCAACATATGATGCATGGACTCAGCTAATA
AATGACACTCAAAAACAACTTCTCATTGGCTCATTTTATTGGACATTAAAATCTGATGAA
GTTTATAATCATTCATCATCAATTTATGGCGATAAAATTTTTCATTCATTACTTAATGCT
GGAACAGAGCGAAAGATTGATATTCGAATTGCACAAAATATGCCATCACAAGTATCACCG
AATATTGATACAGAAATTTTTCAAAAACGTAAAGCGGCAAAAGTACGAAGTGTAAATTTT
CCTCGTCTTCTTGGTGGTGGCGTATTGCATACAAAATTGTGGATTAGTGATAATAAACAT
TTTTATATTGGTAGTGCAAATATGGATTGGCGATCATTGTCACAAGTTAAAGAACTCGGT
GTACTTGTCAATAATTGCTCATGTCTCACAAAAGATTTAACAAAAATTTTCAATATTTAT
TGGGAACTTGGTCGAAATGATTCTGTAATTCCAAGTAAATGGTCAGATAAATTTAATACA
GGAATAAATATGGATAAACCAATGCTCGTGAATTATAACAATAACTACCTATTTAGTACC
TTCTTTTCAAACTCACCACCTCCACTTAACGCTAAAGGAAGAACAAATGATCTTGATGCT
ATTGTACACACTATTCTTAGTGCTGAAAAATATGTAAAAATTTCTGTGATGGATTATTTT
CCTCTTCAGTTGTATTCACCTAAAATAACCTATTGGGGTGAAATTGACAATGCATTGCGA
ACAGCAGCTATTAATAATCGTGTATCAGTAAAACTATTGATCTCATATTGGAATCATTCA
CGACCATCAGAAGATTATTTCTTAAAATCATTAACAGATTTAAGTGGTTCATATAAAGGA
GTCGACATTCAAGTGAAACGATTCATAGTACCAGCAACAGAAGAACAAAAGAAAATTCCA
TTTGGAAGAGTGAATCATAATAAATATATGGTAACGGATCAAGTTGCTTATATTGGAACA
AGCAATTGGTCAGGCGATTATTTCACAAATACAGCTGGAGTTGGTTTTGTTGCCCAAGAT
ACAGTAAATGATAGAAGTGATAATGTGACTACATTGAGAAGTCAGTTAGATTCAATTTTT
GAGAGAGATTGGAACAGTAAATATGCTGTGAATCAAGACAAACTAGAAAGTTAA

>g13640.t1 Gene=g13640 Length=517
MKIFAVNTEVEKDLKKLTVLESNNRDLNQVPVGDDDFELWDYSQMLRNQQRYKWNNNGMV
CKPSCIPIFFILILIVLVVLLPLLDSHNDNKVLGRNGTIIGWNCVDECSIQLVESIPEGL
VYDPDSPSFMSTYDAWTQLINDTQKQLLIGSFYWTLKSDEVYNHSSSIYGDKIFHSLLNA
GTERKIDIRIAQNMPSQVSPNIDTEIFQKRKAAKVRSVNFPRLLGGGVLHTKLWISDNKH
FYIGSANMDWRSLSQVKELGVLVNNCSCLTKDLTKIFNIYWELGRNDSVIPSKWSDKFNT
GINMDKPMLVNYNNNYLFSTFFSNSPPPLNAKGRTNDLDAIVHTILSAEKYVKISVMDYF
PLQLYSPKITYWGEIDNALRTAAINNRVSVKLLISYWNHSRPSEDYFLKSLTDLSGSYKG
VDIQVKRFIVPATEEQKKIPFGRVNHNKYMVTDQVAYIGTSNWSGDYFTNTAGVGFVAQD
TVNDRSDNVTTLRSQLDSIFERDWNSKYAVNQDKLES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13640.t1 CDD cd09106 PLDc_vPLD3_4_5_like_1 112 266 3.46776E-72
11 g13640.t1 CDD cd09107 PLDc_vPLD3_4_5_like_2 321 505 2.07016E-86
6 g13640.t1 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A 122 283 2.7E-22
7 g13640.t1 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A 324 516 1.0E-20
3 g13640.t1 PANTHER PTHR10185 PHOSPHOLIPASE D - RELATED 57 514 4.5E-163
2 g13640.t1 Pfam PF00614 Phospholipase D Active site motif 226 252 5.7E-9
1 g13640.t1 Pfam PF13918 PLD-like domain 255 431 1.0E-36
8 g13640.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 64 -
10 g13640.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 65 84 -
9 g13640.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 85 517 -
16 g13640.t1 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile. 225 252 13.712
17 g13640.t1 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile. 441 467 11.942
14 g13640.t1 SMART SM00155 pld_4 225 252 1.9E-10
15 g13640.t1 SMART SM00155 pld_4 441 467 5.3E-6
5 g13640.t1 SUPERFAMILY SSF56024 Phospholipase D/nuclease 111 283 7.85E-24
4 g13640.t1 SUPERFAMILY SSF56024 Phospholipase D/nuclease 308 513 1.16E-29
13 g13640.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -

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

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