General information for g2288.t1
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.t1 | TSS | g2288.t1 | 16492724 | 16492724 |
| chr_3 | g2288 | g2288.t1 | isoform | g2288.t1 | 16493310 | 16496311 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon1 | 16493310 | 16493448 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS1 | 16493310 | 16493448 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon2 | 16493580 | 16494234 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS2 | 16493580 | 16494234 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon3 | 16494300 | 16494482 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS3 | 16494300 | 16494482 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon4 | 16494544 | 16494755 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS4 | 16494544 | 16494755 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon5 | 16494812 | 16495982 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS5 | 16494812 | 16495982 |
| chr_3 | g2288 | g2288.t1 | exon | g2288.t1.exon6 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t1 | cds | g2288.t1.CDS6 | 16496041 | 16496311 |
| chr_3 | g2288 | g2288.t1 | TTS | g2288.t1 | 16496465 | 16496465 |
Sequences
>g2288.t1 Gene=g2288 Length=2631
ATGGAAGATAAAAAGAAAATAAAAAAACTTAAGAAGAGTGATGAGAAAGGCGATGCAAAA
GATAAACCGAAGCCTTCAGAAGAAGGAGATCAAAAGAAAGTTGGAAGAGGACGAGGCTTT
GAGTCCAGCAGTGATTCAGGTAGTGGAAGTGGCACAACGGAGAGCGATAAAGCAACTGGT
TCTACACCTTCAAGTGGCACAAAAGACTCTAAACAACAATCAGATGTTACTATGAAAACC
ATCGAATCTGAAGATCGAAAAGATGGCCGAAGATTATGGCTCCAATCAGAAACATATAAG
ACACGACCCGAATCATACGATACTTCTTCGTTCAAACCGGTTGAAAACGATCCCAATAAG
AAGTTTGTGGCAAATTACTTTAGACTTAACCAAATGAAGGAATTTGAATTTGTTCAGTAC
CGCATTGACATCATTCCGGAAACGGATGAAAAAAATATTCGACGTGCTTTGATCGCAAAA
TGTCGTTCACATTTGAAAGGATATGTTTTTGATGGTGGTAGCATGATTTTTGTAACACGT
CCTCTTCAGTCAGATCCACTTGAAATTGCTACACGCCTTGATAACAACCCAACTGAATAC
AAATTGATTTTTCGAAAAACTAACTTGCTAATAAATCAAGCTGACGGAACAGCTTTACAT
GTATTCAATGTGATACTAAGAAAAGCAATGGCTGGTTTAAATTTGAAAGAGATTCAACGT
CACCTTTATGATATAAGAGCTAAAATACAATTGCCAGAGTTCAAATTAGAATTATTACCC
GGTTACATCACAAGTATTCGTAAACATGAACAAGATATTTTGATCTGTACCGAAATTACG
CATAAAGTTATGAGGCAAGAGACTTTGCTTCAGATATTGACAGATTTTGTAAAACGTGGT
GGTGATTACCGCAGTGAATTTCAACGTGAAGTAGTTGGAACGGTAGTGATGACACCTTAT
AATTCCAAGACTTATCGCATTGATGATGTTAAATTTGACGCAAATCCACGGAACACTTTT
GATATGAGAGGTACACAAAAATCGTTTGCTGACTATTATTTGGAACGTTACAATATAAAA
TTGAAAGACTTGAATCAACCATTGCTTATTTCAAATCCGAAGGCTCGTGACATTAGAGGA
GGTCGCACAGATCCAGTAATTTTGATTCCTGAACTCTGTGTTGCTACAGGACTTACTGAT
GCAATGCGTACAAATTTTCATATGATGCGTGCAATGGGCGAGTATACACGTTTGAATCCT
TTTAATCGAGCAAAAGTACTAAAAGAATTTTCACGACGAATTAATCAATCTGAAGCAAGT
CAAGATGTTTTGGAATCATTCGGATTAGAGATGGAACGTGATTTAGTTCAATTAGGTGGT
CGTGTTATTAATCCGGAGAAAATCATTTTCGGTAATGATAGAACATTTCAAAATGATAAA
AATGCCGATTGGACGAATGCTATTCGTTCAAACACTATGTGGAATACTCAGTCATTGTCT
CGATGGGGAATCGTATATCCTGTCAGAATGAACAGTGATGTTATTGAATTTATGAAAATT
TTTAGAGACGTAGCACGAGGACAACGATTTGAAGTTTCAGAACCGAAAGAAATTAAATTA
CCTGATGATCGCAGTGGAACTTATGCTAAAGCTTTAGAGGAATTTTGTAGTAAAGATCCG
AAATTTGTTATGATTTTCTTGCCGAATAACAAAGCTGATCTCTACAAGATTATTAAGAAC
ATTACTTATGTGAAATTGGCAATTCCAAATCAAGTTTGTTGTTTGAAAACAATTCAACCA
AAAAAAGGCAACTGGGCTGGAGTAAAATCGATTGCAACAAAAATTCTTCTTCAAATGAAT
TGCAAATTGGGCGGTATTCCTTGGATGATTGGTATACCAATGAAGGGAGTAATGGTAATT
GGTTTTGATGTAACTCATGATACAGCTACAAAATCACATTCATATGGAGCTTTTGTTGCA
AGTATGGACTTGAGAGAATCAGTTAAGTATTATAGCGCTGTTTCAAAACATCAAAACGGT
CAAGAAATTGCAGGAAATATTGCAATTCATTTTCAACAAGCTTTGATTACTTTTAAACGA
GAACATGGTACTTTACCTGATCGTATAATTTTCTATCGTGATGGCGTTGGCGATGGACAA
ATTGAATTTGTTCATACATATGAAGTTCAGAAAATTAGAGATGTGCTCAAAACAAATTAT
GGAGAGATTAAACCAAAATTTGCGTTCGTCATTGTAAGTAAGCGTATTAACACACGATTC
TTTGAAATACATCAACAAGGACAATATGAAAATCCTGTTCCTGGAACTGTTATCGATAAT
ACTATTACATTACCACAACGTTACGAATTCTTTTTAGTGAGTCAAACTGTAAGACAAGGC
ACAGTATCTCCAACCAATTATAATATCATTTTTGATACTTTTGGTTTACAACCTGATAGA
TTGCAACATTTCACATATAAAATGACTCACCTCTACTACAATTGGACAGGAACAGTTCGT
GTACCAATGGTTGTTCAATATGCACACAAATTATCAATTTTAATAGGTCAATTCCTTCAT
GCTCTTCCAAATAATCATACAAATCTTTGCGAACGGCTATACTTTTTGTAA
>g2288.t1 Gene=g2288 Length=876
MEDKKKIKKLKKSDEKGDAKDKPKPSEEGDQKKVGRGRGFESSSDSGSGSGTTESDKATG
STPSSGTKDSKQQSDVTMKTIESEDRKDGRRLWLQSETYKTRPESYDTSSFKPVENDPNK
KFVANYFRLNQMKEFEFVQYRIDIIPETDEKNIRRALIAKCRSHLKGYVFDGGSMIFVTR
PLQSDPLEIATRLDNNPTEYKLIFRKTNLLINQADGTALHVFNVILRKAMAGLNLKEIQR
HLYDIRAKIQLPEFKLELLPGYITSIRKHEQDILICTEITHKVMRQETLLQILTDFVKRG
GDYRSEFQREVVGTVVMTPYNSKTYRIDDVKFDANPRNTFDMRGTQKSFADYYLERYNIK
LKDLNQPLLISNPKARDIRGGRTDPVILIPELCVATGLTDAMRTNFHMMRAMGEYTRLNP
FNRAKVLKEFSRRINQSEASQDVLESFGLEMERDLVQLGGRVINPEKIIFGNDRTFQNDK
NADWTNAIRSNTMWNTQSLSRWGIVYPVRMNSDVIEFMKIFRDVARGQRFEVSEPKEIKL
PDDRSGTYAKALEEFCSKDPKFVMIFLPNNKADLYKIIKNITYVKLAIPNQVCCLKTIQP
KKGNWAGVKSIATKILLQMNCKLGGIPWMIGIPMKGVMVIGFDVTHDTATKSHSYGAFVA
SMDLRESVKYYSAVSKHQNGQEIAGNIAIHFQQALITFKREHGTLPDRIIFYRDGVGDGQ
IEFVHTYEVQKIRDVLKTNYGEIKPKFAFVIVSKRINTRFFEIHQQGQYENPVPGTVIDN
TITLPQRYEFFLVSQTVRQGTVSPTNYNIIFDTFGLQPDRLQHFTYKMTHLYYNWTGTVR
VPMVVQYAHKLSILIGQFLHALPNNHTNLCERLYFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g2288.t1 | CDD | cd02845 | PAZ_piwi_like | 279 | 399 | 1.16175E-43 |
| 11 | g2288.t1 | CDD | cd04658 | Piwi_piwi-like_Euk | 407 | 857 | 5.09964E-173 |
| 7 | g2288.t1 | Gene3D | G3DSA:2.170.260.10 | paz domain | 286 | 405 | 1.2E-36 |
| 9 | g2288.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 490 | 622 | 1.1E-26 |
| 8 | g2288.t1 | Gene3D | G3DSA:3.30.420.10 | - | 632 | 874 | 8.5E-72 |
| 14 | g2288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 39 | - |
| 17 | g2288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 96 | - |
| 16 | g2288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 77 | - |
| 15 | g2288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 78 | 96 | - |
| 3 | g2288.t1 | PANTHER | PTHR22891 | EUKARYOTIC TRANSLATION INITIATION FACTOR 2C | 46 | 876 | 1.4E-223 |
| 4 | g2288.t1 | PANTHER | PTHR22891:SF164 | PIWI-LIKE PROTEIN 1 | 46 | 876 | 1.4E-223 |
| 2 | g2288.t1 | Pfam | PF02170 | PAZ domain | 302 | 417 | 5.7E-29 |
| 1 | g2288.t1 | Pfam | PF02171 | Piwi domain | 562 | 859 | 2.2E-89 |
| 19 | g2288.t1 | ProSiteProfiles | PS50821 | PAZ domain profile. | 307 | 397 | 24.314 |
| 18 | g2288.t1 | ProSiteProfiles | PS50822 | Piwi domain profile. | 562 | 860 | 52.509 |
| 12 | g2288.t1 | SMART | SM00949 | PAZ_2_a_3 | 287 | 421 | 1.6E-53 |
| 13 | g2288.t1 | SMART | SM00950 | Piwi_a_2 | 562 | 860 | 2.4E-109 |
| 6 | g2288.t1 | SUPERFAMILY | SSF101690 | PAZ domain | 121 | 438 | 1.54E-63 |
| 5 | g2288.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 415 | 876 | 3.29E-109 |
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.
