General information for g818.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Transformer-2 sex-determining protein.
Parent gene
- The parent gene g818 is located on chr_3: 6164337..6174353 (+ 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 | g818 | g818.t20 | TSS | g818.t20 | 6163279 | 6163279 |
| chr_3 | g818 | g818.t20 | isoform | g818.t20 | 6163399 | 6174353 |
| chr_3 | g818 | g818.t20 | exon | g818.t20.exon1 | 6163399 | 6163879 |
| chr_3 | g818 | g818.t20 | exon | g818.t20.exon2 | 6163984 | 6164254 |
| chr_3 | g818 | g818.t20 | cds | g818.t20.CDS1 | 6164086 | 6164254 |
| chr_3 | g818 | g818.t20 | exon | g818.t20.exon3 | 6164341 | 6164746 |
| chr_3 | g818 | g818.t20 | cds | g818.t20.CDS2 | 6164341 | 6164603 |
| chr_3 | g818 | g818.t20 | exon | g818.t20.exon4 | 6174319 | 6174353 |
| chr_3 | g818 | g818.t20 | TTS | g818.t20 | NA | NA |
Sequences
>g818.t20 Gene=g818 Length=1193
ATGTCGCGCGACAATCATTTGTGAGTTTTGGGTTGATTGATGACGAATTTAGGGGTTTTA
AAATTTCGCTTTTTCTTTATCTTCTTTTTGTTTTTATTTTTTCATCAACTTCCCGTCATT
GCTAAATAAAATACATCAGACAAAGATCGAGAAGCCGCTCACTTTCCAGATACCGCAATT
ACAAGTGCGTTTCAAATACAAATTCTTCAAATTGCCTGTACAAATCCAACAACAATTCAA
TAATTTCAAAATCAAATTTTCAATTTCTAGCAGTACCTCGAAATCACAACGAACAACCAC
ACCACCGCAATTTTCATCATCATCGTCCTACAGATATAATTCTCGCCATGAGTCACCACC
ATCAAAGCGATCGAGATATCAAAAGGAACGCAGTCGTTCGTTTGAAAAGAATGGAAGCAG
CGGTGGACGAACCAGAAGACGCAATTCACCAGCGACAACCGATATAAGTCGTAAAAATCA
TGAGCCCTCTAGAGTTTTGGGCGTCTTTAATTTGCATGTTCGCACGACTGAGGATGAAAT
TCGTGAAGTTTTCGAACGTTTTGGAGAAATTGACAATATTGTTATGGTAAAAGATGCAAA
AACAAGAGGATTTCGAGGCTATTGCTTTTTGTATTACAATAAGCAACGAGATGCAACAGC
TGCCTTAGAGGAATGCAATGGTATAGAGATCAAAGATCGGCAAATTCGCGTAGATTATTC
ATTAAGTGAAGGTCCTCATGTGAGCACTCCAGGAGAATATCGAGGAAAACGGGGAAGAGA
TAATATGCGCGGCCAAAGACCACGTCATTTAAGTCCATTGCGTGGAGAGAGAACTCGTTA
TTACGATAGATATGACAATGTTCGAACTCGCTCGCGTGATAGAGACAGATATGACAACGA
TCGTTTTAGACGTTCACCGCCTCGTAATTATGATAGATCTGATTATCATCGTCGTGGATC
ACCTGATCGCTTTGATCGCCGAAGATCCCCACCAATGCGTGAACGCAGGCACTAAATATT
TGACTAAAACATGTGTTGATTGAATTTGATGAAGCAAGAGAAGAAACATTTTAACTTACT
ACACACATACAATGAAGATAAAATATATATATCATTTTGCAAAAAAAGCAATTAATTTTA
ACACGGTTTTTTTGCTATTGCTATCATGATAAATCAAATGGGAATAAAATTTT
>g818.t20 Gene=g818 Length=143
MVKDAKTRGFRGYCFLYYNKQRDATAALEECNGIEIKDRQIRVDYSLSEGPHVSTPGEYR
GKRGRDNMRGQRPRHLSPLRGERTRYYDRYDNVRTRSRDRDRYDNDRFRRSPPRNYDRSD
YHRRGSPDRFDRRRSPPMRERRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g818.t20 | Gene3D | G3DSA:3.30.70.330 | - | 1 | 136 | 9.8E-12 |
| 5 | g818.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 143 | - |
| 6 | g818.t20 | MobiDBLite | mobidb-lite | consensus disorder prediction | 56 | 135 | - |
| 2 | g818.t20 | PANTHER | PTHR48034 | TRANSFORMER-2 SEX-DETERMINING PROTEIN-RELATED | 1 | 127 | 3.6E-12 |
| 3 | g818.t20 | PANTHER | PTHR48034:SF6 | TRANSFORMER-2 SEX-DETERMINING PROTEIN | 1 | 127 | 3.6E-12 |
| 1 | g818.t20 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 1 | 42 | 1.8E-8 |
| 8 | g818.t20 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 1 | 48 | 9.678 |
| 4 | g818.t20 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 1 | 74 | 1.9E-15 |
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.
