General information for g2288.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Piwi-like protein Siwi.
Parent gene
- The parent gene g2288 is located on chr_3: 16495336..16496311 (+ 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_3 | g2288 | g2288.t4 | isoform | g2288.t4 | 16495336 | 16496311 |
| chr_3 | g2288 | g2288.t4 | exon | g2288.t4.exon1 | 16495336 | 16495982 |
| chr_3 | g2288 | g2288.t4 | cds | g2288.t4.CDS1 | 16495477 | 16495982 |
| chr_3 | g2288 | g2288.t4 | exon | g2288.t4.exon2 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t4 | cds | g2288.t4.CDS2 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t4 | TTS | g2288.t4 | 16496465 | 16496465 |
| chr_3 | g2288 | g2288.t4 | TSS | g2288.t4 | NA | NA |
Sequences
>g2288.t4 Gene=g2288 Length=918
GCTGATCTCTACAAGATTATTAAGAACATTACTTATGTGAAATTGGCAATTCCAAATCAA
GTTTGTTGTTTGAAAACAATTCAACCAAAAAAAGGCAACTGGGCTGGAGTAAAATCGATT
GCAACAAAAATTCTTCTTCAAATGAATTGCAAATTGGGCGGTATTCCTTGGATGATTGGT
ATACCAATGAAGGGAGTAATGGTAATTGGTTTTGATGTAACTCATGATACAGCTACAAAA
TCACATTCATATGGAGCTTTTGTTGCAAGTATGGACTTGAGAGAATCAGTTAAGTATTAT
AGCGCTGTTTCAAAACATCAAAACGGTCAAGAAATTGCAGGAAATATTGCAATTCATTTT
CAACAAGCTTTGATTACTTTTAAACGAGAACATGGTACTTTACCTGATCGTATAATTTTC
TATCGTGATGGCGTTGGCGATGGACAAATTGAATTTGTTCATACATATGAAGTTCAGAAA
ATTAGAGATGTGCTCAAAACAAATTATGGAGAGATTAAACCAAAATTTGCGTTCGTCATT
GTAAGTAAGCGTATTAACACACGATTCTTTGAAATACATCAACAAGGACAATATGAAAAT
CCTGTTCCTGGAACTGTTATCGATAATACTATTACATTACCACAACGTTACGAATTCTTT
TTAGTGAGTCAAACTGTAAGACAAGGCACAGTATCTCCAACCAATTATAATATCATTTTT
GATACTTTTGGTTTACAACCTGATAGATTGCAACATTTCACATATAAAATGACTCACCTC
TACTACAATTGGACAGGAACAGTTCGTGTACCAATGGTTGTTCAATATGCACACAAATTA
TCAATTTTAATAGGTCAATTCCTTCATGCTCTTCCAAATAATCATACAAATCTTTGCGAA
CGGCTATACTTTTTGTAA
>g2288.t4 Gene=g2288 Length=258
MNCKLGGIPWMIGIPMKGVMVIGFDVTHDTATKSHSYGAFVASMDLRESVKYYSAVSKHQ
NGQEIAGNIAIHFQQALITFKREHGTLPDRIIFYRDGVGDGQIEFVHTYEVQKIRDVLKT
NYGEIKPKFAFVIVSKRINTRFFEIHQQGQYENPVPGTVIDNTITLPQRYEFFLVSQTVR
QGTVSPTNYNIIFDTFGLQPDRLQHFTYKMTHLYYNWTGTVRVPMVVQYAHKLSILIGQF
LHALPNNHTNLCERLYFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2288.t4 | CDD | cd04658 | Piwi_piwi-like_Euk | 1 | 239 | 0.000 |
| 6 | g2288.t4 | Gene3D | G3DSA:3.30.420.10 | - | 14 | 257 | 0.000 |
| 2 | g2288.t4 | PANTHER | PTHR22891 | EUKARYOTIC TRANSLATION INITIATION FACTOR 2C | 1 | 258 | 0.000 |
| 3 | g2288.t4 | PANTHER | PTHR22891:SF164 | PIWI-LIKE PROTEIN 1 | 1 | 258 | 0.000 |
| 1 | g2288.t4 | Pfam | PF02171 | Piwi domain | 1 | 241 | 0.000 |
| 7 | g2288.t4 | ProSiteProfiles | PS50822 | Piwi domain profile. | 1 | 242 | 45.239 |
| 5 | g2288.t4 | SMART | SM00950 | Piwi_a_2 | 1 | 242 | 0.000 |
| 4 | g2288.t4 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 1 | 258 | 0.000 |
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:0003676 | nucleic acid binding | 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.
