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.t2 TSS g13640.t2 31382528 31382528
chr_1 g13640 g13640.t2 isoform g13640.t2 31382831 31392773
chr_1 g13640 g13640.t2 exon g13640.t2.exon1 31382831 31383196
chr_1 g13640 g13640.t2 cds g13640.t2.CDS1 31382831 31383196
chr_1 g13640 g13640.t2 exon g13640.t2.exon2 31390909 31391183
chr_1 g13640 g13640.t2 cds g13640.t2.CDS2 31390909 31391183
chr_1 g13640 g13640.t2 exon g13640.t2.exon3 31391428 31392210
chr_1 g13640 g13640.t2 cds g13640.t2.CDS3 31391428 31392210
chr_1 g13640 g13640.t2 exon g13640.t2.exon4 31392269 31392434
chr_1 g13640 g13640.t2 cds g13640.t2.CDS4 31392269 31392434
chr_1 g13640 g13640.t2 exon g13640.t2.exon5 31392495 31392773
chr_1 g13640 g13640.t2 cds g13640.t2.CDS5 31392495 31392773
chr_1 g13640 g13640.t2 TTS g13640.t2 31393035 31393035

Sequences

>g13640.t2 Gene=g13640 Length=1869
ATGCCAGTATCTGGATTTTGGGATTATATTCACATTGGACGATCACGAACAAGTAATGAT
GATGATGAAGACCCAACGGCACATAACTTGCAAGAAGGACTTTTTCAAATTGCTTCACAG
ACATGCAATATTCTTGTACAAGTTAATAATACAAATAATATAAATTTGGGTTCAAGTTTT
AATTATAAGGATTTTGAAACAAAACAATTTTCATCAAAATATGGAGAGTCATCGAATTCA
CGAGATGTGGCGAACAAAAATACATTCTTTGACCTGGAATCAAGCGTTGTTTTGCTTCAG
CCAAAGCAGTCAACGCCAACCAAAGTTCGCTTTTCTCGTCTGTCTGAATACAAACGTCGA
TTATCTACAGTACTCGAGTCAAATAATCGCGATCTCAATCAAGTTCCTGTTGGTGACGAT
GATTTTGAACTGTGGGATTATTCACAAATGTTGAGGAATCAGCAACGATATAAGTGGAAT
AATAATGGAATGGTTTGCAAGCCTTCCTGCATTCCTATTTTTTTCATCCTCATTCTTATC
GTTCTCGTTGTGCTTCTTCCACTTCTCGATTCGCATAACGATAACAAAGTGTTGGGTCGA
AATGGTACAATAATTGGTTGGAATTGTGTAGATGAATGCAGCATTCAACTGGTCGAATCA
ATTCCAGAAGGTTTAGTTTATGATCCTGACAGTCCATCATTTATGTCAACATATGATGCA
TGGACTCAGCTAATAAATGACACTCAAAAACAACTTCTCATTGGCTCATTTTATTGGACA
TTAAAATCTGATGAAGTTTATAATCATTCATCATCAATTTATGGCGATAAAATTTTTCAT
TCATTACTTAATGCTGGAACAGAGCGAAAGATTGATATTCGAATTGCACAAAATATGCCA
TCACAAGTATCACCGAATATTGATACAGAAATTTTTCAAAAACGTAAAGCGGCAAAAGTA
CGAAGTGTAAATTTTCCTCGTCTTCTTGGTGGTGGCGTATTGCATACAAAATTGTGGATT
AGTGATAATAAACATTTTTATATTGGTAGTGCAAATATGGATTGGCGATCATTGTCACAA
GTTAAAGAACTCGGTGTACTTGTCAATAATTGCTCATGTCTCACAAAAGATTTAACAAAA
ATTTTCAATATTTATTGGGAACTTGGTCGAAATGATTCTGTAATTCCAAGTAAATGGTCA
GATAAATTTAATACAGGAATAAATATGGATAAACCAATGCTCGTGAATTATAACAATAAC
TACCTATTTAGTACCTTCTTTTCAAACTCACCACCTCCACTTAACGCTAAAGGAAGAACA
AATGATCTTGATGCTATTGTACACACTATTCTTAGTGCTGAAAAATATGTAAAAATTTCT
GTGATGGATTATTTTCCTCTTCAGTTGTATTCACCTAAAATAACCTATTGGGGTGAAATT
GACAATGCATTGCGAACAGCAGCTATTAATAATCGTGTATCAGTAAAACTATTGATCTCA
TATTGGAATCATTCACGACCATCAGAAGATTATTTCTTAAAATCATTAACAGATTTAAGT
GGTTCATATAAAGGAGTCGACATTCAAGTGAAACGATTCATAGTACCAGCAACAGAAGAA
CAAAAGAAAATTCCATTTGGAAGAGTGAATCATAATAAATATATGGTAACGGATCAAGTT
GCTTATATTGGAACAAGCAATTGGTCAGGCGATTATTTCACAAATACAGCTGGAGTTGGT
TTTGTTGCCCAAGATACAGTAAATGATAGAAGTGATAATGTGACTACATTGAGAAGTCAG
TTAGATTCAATTTTTGAGAGAGATTGGAACAGTAAATATGCTGTGAATCAAGACAAACTA
GAAAGTTAA

>g13640.t2 Gene=g13640 Length=622
MPVSGFWDYIHIGRSRTSNDDDEDPTAHNLQEGLFQIASQTCNILVQVNNTNNINLGSSF
NYKDFETKQFSSKYGESSNSRDVANKNTFFDLESSVVLLQPKQSTPTKVRFSRLSEYKRR
LSTVLESNNRDLNQVPVGDDDFELWDYSQMLRNQQRYKWNNNGMVCKPSCIPIFFILILI
VLVVLLPLLDSHNDNKVLGRNGTIIGWNCVDECSIQLVESIPEGLVYDPDSPSFMSTYDA
WTQLINDTQKQLLIGSFYWTLKSDEVYNHSSSIYGDKIFHSLLNAGTERKIDIRIAQNMP
SQVSPNIDTEIFQKRKAAKVRSVNFPRLLGGGVLHTKLWISDNKHFYIGSANMDWRSLSQ
VKELGVLVNNCSCLTKDLTKIFNIYWELGRNDSVIPSKWSDKFNTGINMDKPMLVNYNNN
YLFSTFFSNSPPPLNAKGRTNDLDAIVHTILSAEKYVKISVMDYFPLQLYSPKITYWGEI
DNALRTAAINNRVSVKLLISYWNHSRPSEDYFLKSLTDLSGSYKGVDIQVKRFIVPATEE
QKKIPFGRVNHNKYMVTDQVAYIGTSNWSGDYFTNTAGVGFVAQDTVNDRSDNVTTLRSQ
LDSIFERDWNSKYAVNQDKLES

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g13640.t2 CDD cd09106 PLDc_vPLD3_4_5_like_1 217 371 3.30655E-71
11 g13640.t2 CDD cd09107 PLDc_vPLD3_4_5_like_2 426 610 3.41642E-85
6 g13640.t2 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A 227 388 3.8E-22
7 g13640.t2 Gene3D G3DSA:3.30.870.10 Endonuclease Chain A 429 621 1.5E-20
3 g13640.t2 PANTHER PTHR10185 PHOSPHOLIPASE D - RELATED 162 619 7.9E-163
2 g13640.t2 Pfam PF00614 Phospholipase D Active site motif 331 357 7.2E-9
1 g13640.t2 Pfam PF13918 PLD-like domain 360 536 1.5E-36
9 g13640.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 170 -
10 g13640.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 189 -
8 g13640.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 190 622 -
17 g13640.t2 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile. 330 357 13.712
16 g13640.t2 ProSiteProfiles PS50035 Phospholipase D phosphodiesterase active site profile. 546 572 11.942
15 g13640.t2 SMART SM00155 pld_4 330 357 1.9E-10
14 g13640.t2 SMART SM00155 pld_4 546 572 5.3E-6
4 g13640.t2 SUPERFAMILY SSF56024 Phospholipase D/nuclease 217 388 1.21E-23
5 g13640.t2 SUPERFAMILY SSF56024 Phospholipase D/nuclease 413 618 1.76E-29
13 g13640.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 164 186 -

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