General information for g2288.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein aubergine.
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.t3 | isoform | g2288.t3 | 16494544 | 16496311 |
| chr_3 | g2288 | g2288.t3 | exon | g2288.t3.exon1 | 16494544 | 16494755 |
| chr_3 | g2288 | g2288.t3 | cds | g2288.t3.CDS1 | 16494590 | 16494755 |
| chr_3 | g2288 | g2288.t3 | exon | g2288.t3.exon2 | 16494812 | 16495982 |
| chr_3 | g2288 | g2288.t3 | cds | g2288.t3.CDS2 | 16494812 | 16495982 |
| chr_3 | g2288 | g2288.t3 | exon | g2288.t3.exon3 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t3 | cds | g2288.t3.CDS3 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t3 | TTS | g2288.t3 | 16496465 | 16496465 |
| chr_3 | g2288 | g2288.t3 | TSS | g2288.t3 | NA | NA |
Sequences
>g2288.t3 Gene=g2288 Length=1654
CATTGATGATGTTAAATTTGACGCAAATCCACGGAACACTTTTGATATGAGAGGTACACA
AAAATCGTTTGCTGACTATTATTTGGAACGTTACAATATAAAATTGAAAGACTTGAATCA
ACCATTGCTTATTTCAAATCCGAAGGCTCGTGACATTAGAGGAGGTCGCACAGATCCAGT
AATTTTGATTCCTGAACTCTGTGTTGCTACAGGACTTACTGATGCAATGCGTACAAATTT
TCATATGATGCGTGCAATGGGCGAGTATACACGTTTGAATCCTTTTAATCGAGCAAAAGT
ACTAAAAGAATTTTCACGACGAATTAATCAATCTGAAGCAAGTCAAGATGTTTTGGAATC
ATTCGGATTAGAGATGGAACGTGATTTAGTTCAATTAGGTGGTCGTGTTATTAATCCGGA
GAAAATCATTTTCGGTAATGATAGAACATTTCAAAATGATAAAAATGCCGATTGGACGAA
TGCTATTCGTTCAAACACTATGTGGAATACTCAGTCATTGTCTCGATGGGGAATCGTATA
TCCTGTCAGAATGAACAGTGATGTTATTGAATTTATGAAAATTTTTAGAGACGTAGCACG
AGGACAACGATTTGAAGTTTCAGAACCGAAAGAAATTAAATTACCTGATGATCGCAGTGG
AACTTATGCTAAAGCTTTAGAGGAATTTTGTAGTAAAGATCCGAAATTTGTTATGATTTT
CTTGCCGAATAACAAAGCTGATCTCTACAAGATTATTAAGAACATTACTTATGTGAAATT
GGCAATTCCAAATCAAGTTTGTTGTTTGAAAACAATTCAACCAAAAAAAGGCAACTGGGC
TGGAGTAAAATCGATTGCAACAAAAATTCTTCTTCAAATGAATTGCAAATTGGGCGGTAT
TCCTTGGATGATTGGTATACCAATGAAGGGAGTAATGGTAATTGGTTTTGATGTAACTCA
TGATACAGCTACAAAATCACATTCATATGGAGCTTTTGTTGCAAGTATGGACTTGAGAGA
ATCAGTTAAGTATTATAGCGCTGTTTCAAAACATCAAAACGGTCAAGAAATTGCAGGAAA
TATTGCAATTCATTTTCAACAAGCTTTGATTACTTTTAAACGAGAACATGGTACTTTACC
TGATCGTATAATTTTCTATCGTGATGGCGTTGGCGATGGACAAATTGAATTTGTTCATAC
ATATGAAGTTCAGAAAATTAGAGATGTGCTCAAAACAAATTATGGAGAGATTAAACCAAA
ATTTGCGTTCGTCATTGTAAGTAAGCGTATTAACACACGATTCTTTGAAATACATCAACA
AGGACAATATGAAAATCCTGTTCCTGGAACTGTTATCGATAATACTATTACATTACCACA
ACGTTACGAATTCTTTTTAGTGAGTCAAACTGTAAGACAAGGCACAGTATCTCCAACCAA
TTATAATATCATTTTTGATACTTTTGGTTTACAACCTGATAGATTGCAACATTTCACATA
TAAAATGACTCACCTCTACTACAATTGGACAGGAACAGTTCGTGTACCAATGGTTGTTCA
ATATGCACACAAATTATCAATTTTAATAGGTCAATTCCTTCATGCTCTTCCAAATAATCA
TACAAATCTTTGCGAACGGCTATACTTTTTGTAA
>g2288.t3 Gene=g2288 Length=535
MRGTQKSFADYYLERYNIKLKDLNQPLLISNPKARDIRGGRTDPVILIPELCVATGLTDA
MRTNFHMMRAMGEYTRLNPFNRAKVLKEFSRRINQSEASQDVLESFGLEMERDLVQLGGR
VINPEKIIFGNDRTFQNDKNADWTNAIRSNTMWNTQSLSRWGIVYPVRMNSDVIEFMKIF
RDVARGQRFEVSEPKEIKLPDDRSGTYAKALEEFCSKDPKFVMIFLPNNKADLYKIIKNI
TYVKLAIPNQVCCLKTIQPKKGNWAGVKSIATKILLQMNCKLGGIPWMIGIPMKGVMVIG
FDVTHDTATKSHSYGAFVASMDLRESVKYYSAVSKHQNGQEIAGNIAIHFQQALITFKRE
HGTLPDRIIFYRDGVGDGQIEFVHTYEVQKIRDVLKTNYGEIKPKFAFVIVSKRINTRFF
EIHQQGQYENPVPGTVIDNTITLPQRYEFFLVSQTVRQGTVSPTNYNIIFDTFGLQPDRL
QHFTYKMTHLYYNWTGTVRVPMVVQYAHKLSILIGQFLHALPNNHTNLCERLYFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g2288.t3 | CDD | cd04658 | Piwi_piwi-like_Euk | 66 | 516 | 0.0000000 |
| 9 | g2288.t3 | Gene3D | G3DSA:2.170.260.10 | paz domain | 1 | 64 | 0.0000000 |
| 11 | g2288.t3 | Gene3D | G3DSA:3.40.50.2300 | - | 149 | 281 | 0.0000000 |
| 10 | g2288.t3 | Gene3D | G3DSA:3.30.420.10 | - | 291 | 533 | 0.0000000 |
| 3 | g2288.t3 | PANTHER | PTHR22891 | EUKARYOTIC TRANSLATION INITIATION FACTOR 2C | 3 | 535 | 0.0000000 |
| 4 | g2288.t3 | PANTHER | PTHR22891:SF164 | PIWI-LIKE PROTEIN 1 | 3 | 535 | 0.0000000 |
| 2 | g2288.t3 | Pfam | PF02170 | PAZ domain | 4 | 76 | 0.0000000 |
| 1 | g2288.t3 | Pfam | PF02171 | Piwi domain | 221 | 518 | 0.0000000 |
| 13 | g2288.t3 | ProSiteProfiles | PS50821 | PAZ domain profile. | 2 | 56 | 15.9410000 |
| 12 | g2288.t3 | ProSiteProfiles | PS50822 | Piwi domain profile. | 221 | 519 | 52.5090000 |
| 7 | g2288.t3 | SMART | SM00949 | PAZ_2_a_3 | 1 | 80 | 0.0000074 |
| 8 | g2288.t3 | SMART | SM00950 | Piwi_a_2 | 221 | 519 | 0.0000000 |
| 6 | g2288.t3 | SUPERFAMILY | SSF101690 | PAZ domain | 3 | 97 | 0.0000000 |
| 5 | g2288.t3 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 74 | 535 | 0.0000000 |
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:0005515 | protein binding | MF |
| 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.
