General information for g12842.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein aubergine.
Parent gene
- The parent gene g12842 is located on chr_1: 26502812..26504198 (- 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 | g12842 | g12842.t1 | TTS | g12842.t1 | 26502085 | 26502085 |
| chr_1 | g12842 | g12842.t1 | isoform | g12842.t1 | 26502812 | 26504198 |
| chr_1 | g12842 | g12842.t1 | exon | g12842.t1.exon1 | 26502812 | 26503548 |
| chr_1 | g12842 | g12842.t1 | cds | g12842.t1.CDS1 | 26502812 | 26503548 |
| chr_1 | g12842 | g12842.t1 | exon | g12842.t1.exon2 | 26503607 | 26503784 |
| chr_1 | g12842 | g12842.t1 | cds | g12842.t1.CDS2 | 26503607 | 26503784 |
| chr_1 | g12842 | g12842.t1 | exon | g12842.t1.exon3 | 26503883 | 26504024 |
| chr_1 | g12842 | g12842.t1 | cds | g12842.t1.CDS3 | 26503883 | 26504024 |
| chr_1 | g12842 | g12842.t1 | exon | g12842.t1.exon4 | 26504090 | 26504126 |
| chr_1 | g12842 | g12842.t1 | cds | g12842.t1.CDS4 | 26504090 | 26504126 |
| chr_1 | g12842 | g12842.t1 | exon | g12842.t1.exon5 | 26504192 | 26504198 |
| chr_1 | g12842 | g12842.t1 | cds | g12842.t1.CDS5 | 26504192 | 26504198 |
| chr_1 | g12842 | g12842.t1 | TSS | g12842.t1 | NA | NA |
Sequences
>g12842.t1 Gene=g12842 Length=1101
ATGGCTGAGTTCAAATTAGAATTATTACCCGGTTACATCACAAGTATTCGTAAACATGAA
CAAGATATTTTGATCTGTACCGAAATTACACATAAAGATATGAGGCAAGAGACTTTGCTT
CAGATATTGACAGATTTTGTAAGACGTAGTGGTGATTACCGCAGTGAATTTCTCCAAGAC
TTATCGAACACTTTTGATATGAGAGGTACACAAAAATCGTTTGCTGACTATTATTTGGAA
CGTTACAATATAAGATTGAAAGACTTACATCAACCATTGCTTATTTCAAATCCGAAGGCT
CGTGATATTAGAGGAGGTCGCACGGATCAAGTAATTTTGATTCCTGAACTTTGTGTTGCT
ACAGGACTTACTGATGCAATGCGTACAAATTTTTATATGATGCGTGCAATGGGCGAGTAT
ACACGTTTGAATCCTTTTAATCGAGCAAAAGTTCTTAAAGAATTTTCACGACGAATTAAT
CAATCTGAAGCAAGTCAAGATGTTTTGGAATCATTCGGATTAGAGATGGAACGTGATTTA
GTTCAATTAGGTGGTCGTGTTATAAATCCGGAGAAAATCATTTTCGGTAATGATAGAACA
TTTCAAAATGATAAAAATGCCGATTGGACAAATGCTATTCGTTCAAACACTATGTGGAAT
GCTCAGTCATTATCTCGATGGGGAATCGTATATATATATCCTGTCAGAATGAATAGTGAT
GTTATTGAATTTATGAAAATTTTTAGAGACGTAGCACGAGGACAAAGATTCGAAGTTTCA
GAACCGAAAGAAATCAAATTATCTGATGATCGCAGTGGAACTTATGCTAAAGCTTTAGAG
GAATTTTGTAGTAAAGATCCGAAATTTGTTATGATTTTCTTGCCGAATAACAAAGCTGAT
CTCTATAAGATTATTAAGAACATTACTTATGTAAAATTGGCAATTCCAAATCAAATTTTT
TGTTTGAAAACAATTCAACCAAAAAAAAGCAACTGGGCTGGAGTAAAATCGATTGCAACA
AAAATTCTTCTTCAAATGAATTGCAAATTGGGCGGTGTCCCGTGGATGATTGGTATACCG
GGAACATGGTACTTTACCTGA
>g12842.t1 Gene=g12842 Length=366
MAEFKLELLPGYITSIRKHEQDILICTEITHKDMRQETLLQILTDFVRRSGDYRSEFLQD
LSNTFDMRGTQKSFADYYLERYNIRLKDLHQPLLISNPKARDIRGGRTDQVILIPELCVA
TGLTDAMRTNFYMMRAMGEYTRLNPFNRAKVLKEFSRRINQSEASQDVLESFGLEMERDL
VQLGGRVINPEKIIFGNDRTFQNDKNADWTNAIRSNTMWNAQSLSRWGIVYIYPVRMNSD
VIEFMKIFRDVARGQRFEVSEPKEIKLSDDRSGTYAKALEEFCSKDPKFVMIFLPNNKAD
LYKIIKNITYVKLAIPNQIFCLKTIQPKKSNWAGVKSIATKILLQMNCKLGGVPWMIGIP
GTWYFT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12842.t1 | Gene3D | G3DSA:2.170.260.10 | paz domain | 54 | 130 | 0.000 |
| 9 | g12842.t1 | Gene3D | G3DSA:3.40.50.2300 | - | 215 | 349 | 0.000 |
| 3 | g12842.t1 | PANTHER | PTHR22891 | EUKARYOTIC TRANSLATION INITIATION FACTOR 2C | 3 | 360 | 0.000 |
| 4 | g12842.t1 | PANTHER | PTHR22891:SF164 | PIWI-LIKE PROTEIN 1 | 3 | 360 | 0.000 |
| 2 | g12842.t1 | Pfam | PF02170 | PAZ domain | 62 | 142 | 0.000 |
| 1 | g12842.t1 | Pfam | PF02171 | Piwi domain | 289 | 360 | 0.000 |
| 11 | g12842.t1 | ProSiteProfiles | PS50821 | PAZ domain profile. | 64 | 122 | 17.344 |
| 10 | g12842.t1 | ProSiteProfiles | PS50822 | Piwi domain profile. | 289 | 366 | 11.359 |
| 7 | g12842.t1 | SMART | SM00949 | PAZ_2_a_3 | 37 | 146 | 0.000 |
| 6 | g12842.t1 | SUPERFAMILY | SSF101690 | PAZ domain | 4 | 163 | 0.000 |
| 5 | g12842.t1 | SUPERFAMILY | SSF53098 | Ribonuclease H-like | 140 | 360 | 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: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.
