General information for g13640.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 5’-3’ exonuclease PLD3.
Parent gene
- The parent gene g13640 is located on chr_1: 31390318..31392773 (+ strand)
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.t3 | TSS | g13640.t3 | 31390225 | 31390225 |
| chr_1 | g13640 | g13640.t3 | isoform | g13640.t3 | 31390318 | 31392208 |
| chr_1 | g13640 | g13640.t3 | exon | g13640.t3.exon1 | 31390318 | 31390368 |
| chr_1 | g13640 | g13640.t3 | cds | g13640.t3.CDS1 | 31390318 | 31390368 |
| chr_1 | g13640 | g13640.t3 | exon | g13640.t3.exon2 | 31390909 | 31391183 |
| chr_1 | g13640 | g13640.t3 | cds | g13640.t3.CDS2 | 31390909 | 31391183 |
| chr_1 | g13640 | g13640.t3 | exon | g13640.t3.exon3 | 31391428 | 31392208 |
| chr_1 | g13640 | g13640.t3 | cds | g13640.t3.CDS3 | 31391428 | 31392208 |
| chr_1 | g13640 | g13640.t3 | TTS | g13640.t3 | 31393035 | 31393035 |
Sequences
>g13640.t3 Gene=g13640 Length=1107
ATGAAAATTTTTGCGGTTAATACTGAAGTTGAAAAGGATTTAAAAAAGCTAACAGTACTC
GAGTCAAATAATCGCGATCTCAATCAAGTTCCTGTTGGTGACGATGATTTTGAACTGTGG
GATTATTCACAAATGTTGAGGAATCAGCAACGATATAAGTGGAATAATAATGGAATGGTT
TGCAAGCCTTCCTGCATTCCTATTTTTTTCATCCTCATTCTTATCGTTCTCGTTGTGCTT
CTTCCACTTCTCGATTCGCATAACGATAACAAAGTGTTGGGTCGAAATGGTACAATAATT
GGTTGGAATTGTGTAGATGAATGCAGCATTCAACTGGTCGAATCAATTCCAGAAGGTTTA
GTTTATGATCCTGACAGTCCATCATTTATGTCAACATATGATGCATGGACTCAGCTAATA
AATGACACTCAAAAACAACTTCTCATTGGCTCATTTTATTGGACATTAAAATCTGATGAA
GTTTATAATCATTCATCATCAATTTATGGCGATAAAATTTTTCATTCATTACTTAATGCT
GGAACAGAGCGAAAGATTGATATTCGAATTGCACAAAATATGCCATCACAAGTATCACCG
AATATTGATACAGAAATTTTTCAAAAACGTAAAGCGGCAAAAGTACGAAGTGTAAATTTT
CCTCGTCTTCTTGGTGGTGGCGTATTGCATACAAAATTGTGGATTAGTGATAATAAACAT
TTTTATATTGGTAGTGCAAATATGGATTGGCGATCATTGTCACAAGTTAAAGAACTCGGT
GTACTTGTCAATAATTGCTCATGTCTCACAAAAGATTTAACAAAAATTTTCAATATTTAT
TGGGAACTTGGTCGAAATGATTCTGTAATTCCAAGTAAATGGTCAGATAAATTTAATACA
GGAATAAATATGGATAAACCAATGCTCGTGAATTATAACAATAACTACCTATTTAGTACC
TTCTTTTCAAACTCACCACCTCCACTTAACGCTAAAGGAAGAACAAATGATCTTGATGCT
ATTGTACACACTATTCTTAGTGCTGAAAAATATGTAAAAATTTCTGTGATGGATTATTTT
CCTCTTCAGTTGTATTCACCTAAAATA
>g13640.t3 Gene=g13640 Length=369
MKIFAVNTEVEKDLKKLTVLESNNRDLNQVPVGDDDFELWDYSQMLRNQQRYKWNNNGMV
CKPSCIPIFFILILIVLVVLLPLLDSHNDNKVLGRNGTIIGWNCVDECSIQLVESIPEGL
VYDPDSPSFMSTYDAWTQLINDTQKQLLIGSFYWTLKSDEVYNHSSSIYGDKIFHSLLNA
GTERKIDIRIAQNMPSQVSPNIDTEIFQKRKAAKVRSVNFPRLLGGGVLHTKLWISDNKH
FYIGSANMDWRSLSQVKELGVLVNNCSCLTKDLTKIFNIYWELGRNDSVIPSKWSDKFNT
GINMDKPMLVNYNNNYLFSTFFSNSPPPLNAKGRTNDLDAIVHTILSAEKYVKISVMDYF
PLQLYSPKI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g13640.t3 | CDD | cd09106 | PLDc_vPLD3_4_5_like_1 | 112 | 266 | 3.44745E-74 |
| 5 | g13640.t3 | Gene3D | G3DSA:3.30.870.10 | Endonuclease Chain A | 122 | 283 | 1.3E-22 |
| 3 | g13640.t3 | PANTHER | PTHR10185 | PHOSPHOLIPASE D - RELATED | 57 | 366 | 9.1E-98 |
| 2 | g13640.t3 | Pfam | PF00614 | Phospholipase D Active site motif | 226 | 252 | 3.8E-9 |
| 1 | g13640.t3 | Pfam | PF13918 | PLD-like domain | 255 | 365 | 9.4E-19 |
| 6 | g13640.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 64 | - |
| 8 | g13640.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 84 | - |
| 7 | g13640.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 85 | 369 | - |
| 12 | g13640.t3 | ProSiteProfiles | PS50035 | Phospholipase D phosphodiesterase active site profile. | 225 | 252 | 13.712 |
| 11 | g13640.t3 | SMART | SM00155 | pld_4 | 225 | 252 | 1.9E-10 |
| 4 | g13640.t3 | SUPERFAMILY | SSF56024 | Phospholipase D/nuclease | 110 | 283 | 3.36E-24 |
| 10 | g13640.t3 | 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
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.
