General information for g5335.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Plasmanylethanolamine desaturase.
Parent gene
- The parent gene g5335 is located on chr_2: 8882656..8886101 (+ 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_2 | g5335 | g5335.t3 | isoform | g5335.t3 | 8880784 | 8886101 |
| chr_2 | g5335 | g5335.t3 | TSS | g5335.t3 | 8880784 | 8880784 |
| chr_2 | g5335 | g5335.t3 | exon | g5335.t3.exon1 | 8880784 | 8880943 |
| chr_2 | g5335 | g5335.t3 | exon | g5335.t3.exon2 | 8882646 | 8882766 |
| chr_2 | g5335 | g5335.t3 | cds | g5335.t3.CDS1 | 8882656 | 8882766 |
| chr_2 | g5335 | g5335.t3 | exon | g5335.t3.exon3 | 8882959 | 8883115 |
| chr_2 | g5335 | g5335.t3 | cds | g5335.t3.CDS2 | 8882959 | 8883115 |
| chr_2 | g5335 | g5335.t3 | exon | g5335.t3.exon4 | 8885349 | 8885949 |
| chr_2 | g5335 | g5335.t3 | cds | g5335.t3.CDS3 | 8885349 | 8885949 |
| chr_2 | g5335 | g5335.t3 | exon | g5335.t3.exon5 | 8886011 | 8886101 |
| chr_2 | g5335 | g5335.t3 | cds | g5335.t3.CDS4 | 8886011 | 8886101 |
| chr_2 | g5335 | g5335.t3 | TTS | g5335.t3 | 8886322 | 8886322 |
Sequences
>g5335.t3 Gene=g5335 Length=1130
CAGTTTAGTTTTGTCATTTGTCGAAAAAAGGTTGAAAAAAGTGAATTCTCCTTTGAATTA
AAAAGAACCGGCAATAAAAAAAGATAAAGTCAAAAAAAATTATGCTCTATCAATCATAAT
TATTGCAATCAATTTCAAAGTTCGTGATAAGAAATTAAAAAATAAAAAATATGGATATCA
TAAGCATTTCTCCCTGCATAAAGCGAACATCAGAAGTGGGTAAAGAAGATTGTCCACACA
TTCCAAGCGTCTCGAAAAGTGAAATTCAAAATTTTCTCACGCCAAGACCAGTAAAAACTG
ATCAAGAAATTATTGAAAGTTCCATGGCTGAAGATGATCCAAATTGCATATCAGAAGATG
AAGACACAACCTTTGAAAAAGTTCGCTGGGGTAGACATCATAAAGGAGCAAAAATTCTTG
CAAATTTTTATAGCAGTGGAAAACGAACACAGGAAATAATCTGCGTCTACTCTTGCATTT
CACTTATGTTTATCAATTTTTATTTTATTCTAAGTCATTTTCGTATGGATTATTTCTCAA
AAGTTGTGCTATCAGGAGTATGTGGAATTTTAACAGCTGATTTTGGTAGTGGTCTTGTTC
ATTGGGGCGCAGATACTTGGGGAAGCATTGAATTGCCGATTATTGGAAAAAACTTTCTTC
GACCTTTTCGTGAACATCACATCGACCCAACGAGCATCACGCGACATGATTGGATTGAGA
CTAATGGTGATAATTTTATGATTGCAATCCCAATTTTATCAAGACTGACTTGGATTTTTT
ATATGACACCCAAGTCTGAAATTCCTGAAGTTTATCCCTTTTGTGCATTCTTATTTCTTT
GTTCAATTTTTGTTGCAATTACAAATCAAATTCACAAATGGTCGCATACTTACTTTGACC
TGCCATTTTGGGTACAAATTCTACAAAACTATCATATCATACTGCCACGAAAACATCATC
GAATTCATCATGTTGCACCTCATGAAACTTACTTTTGTATTACAACTGGGTGGTTAAATT
ATCCTTTAGAAAAAATCAGATTCTGGCCAACATTAGAATCAATTGTGACATTAATAACAG
GCTATAAACCACGTGAAGATGATCTCAAATGGGCATCAAAGACATCGTAA
>g5335.t3 Gene=g5335 Length=319
MDIISISPCIKRTSEVGKEDCPHIPSVSKSEIQNFLTPRPVKTDQEIIESSMAEDDPNCI
SEDEDTTFEKVRWGRHHKGAKILANFYSSGKRTQEIICVYSCISLMFINFYFILSHFRMD
YFSKVVLSGVCGILTADFGSGLVHWGADTWGSIELPIIGKNFLRPFREHHIDPTSITRHD
WIETNGDNFMIAIPILSRLTWIFYMTPKSEIPEVYPFCAFLFLCSIFVAITNQIHKWSHT
YFDLPFWVQILQNYHIILPRKHHRIHHVAPHETYFCITTGWLNYPLEKIRFWPTLESIVT
LITGYKPREDDLKWASKTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5335.t3 | PANTHER | PTHR48177 | TRANSMEMBRANE PROTEIN 189 | 63 | 319 | 2.5E-109 |
| 1 | g5335.t3 | Pfam | PF10520 | B domain of TMEM189, localisation domain | 133 | 310 | 6.2E-75 |
| 6 | g5335.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 95 | - |
| 10 | g5335.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 114 | - |
| 8 | g5335.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 115 | 213 | - |
| 9 | g5335.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 214 | 231 | - |
| 7 | g5335.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 232 | 319 | - |
| 4 | g5335.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 96 | 118 | - |
| 3 | g5335.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 147 | - |
| 5 | g5335.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 211 | 230 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5335/g5335.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5335.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K20656 (plasmanylethanolamine desaturase)
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. There were no conditions that were differentially expressed