General information for g818.t17
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.t17 | TSS | g818.t17 | 6163279 | 6163279 |
| chr_3 | g818 | g818.t17 | isoform | g818.t17 | 6163399 | 6165060 |
| chr_3 | g818 | g818.t17 | exon | g818.t17.exon1 | 6163399 | 6163418 |
| chr_3 | g818 | g818.t17 | cds | g818.t17.CDS1 | 6163399 | 6163418 |
| chr_3 | g818 | g818.t17 | exon | g818.t17.exon2 | 6163538 | 6163582 |
| chr_3 | g818 | g818.t17 | cds | g818.t17.CDS2 | 6163538 | 6163582 |
| chr_3 | g818 | g818.t17 | exon | g818.t17.exon3 | 6163669 | 6163879 |
| chr_3 | g818 | g818.t17 | cds | g818.t17.CDS3 | 6163669 | 6163879 |
| chr_3 | g818 | g818.t17 | exon | g818.t17.exon4 | 6163984 | 6164254 |
| chr_3 | g818 | g818.t17 | cds | g818.t17.CDS4 | 6163984 | 6164254 |
| chr_3 | g818 | g818.t17 | exon | g818.t17.exon5 | 6164344 | 6165060 |
| chr_3 | g818 | g818.t17 | cds | g818.t17.CDS5 | 6164344 | 6164603 |
| chr_3 | g818 | g818.t17 | TTS | g818.t17 | 6165054 | 6165054 |
Sequences
>g818.t17 Gene=g818 Length=1264
ATGTCGCGCGACAATCATTTACAAAGATCGAGAAGCCGCTCACTTTCCAGATACCGCAAT
TACAACAGTACCTCGAAATCACAACGAACAACCACACCACCGCAATTTTCATCATCATCG
TCCTACAGATATAATTCTCGCCATGAGTCACCACCATCAAAGCGATCGAGATATCAAAAG
GAACGCAGTCGTTCGTTTGAAAAGAATGGAAGCAGCGGTGGACGAACCAGAAGACGCAAT
TCACCAGCGACAACCGATATAAGTCGTAAAAATCATGAGCCCTCTAGAGTTTTGGGCGTC
TTTAATTTGCATGTTCGCACGACTGAGGATGAAATTCGTGAAGTTTTCGAACGTTTTGGA
GAAATTGACAATATTGTTATGGTAAAAGATGCAAAAACAAGAGGATTTCGAGGCTATTGC
TTTTTGTATTACAATAAGCAACGAGATGCAACAGCTGCCTTAGAGGAATGCAATGGTATA
GAGATCAAAGATCGGCAAATTCGCGTAGATTATTCATTAAGTGAAGGTCCTCATGTGAGC
ACTCCAGAATATCGAGGAAAACGGGGAAGAGATAATATGCGCGGCCAAAGACCACGTCAT
TTAAGTCCATTGCGTGGAGAGAGAACTCGTTATTACGATAGATATGACAATGTTCGAACT
CGCTCGCGTGATAGAGACAGATATGACAACGATCGTTTTAGACGTTCACCGCCTCGTAAT
TATGATAGATCTGATTATCATCGTCGTGGATCACCTGATCGCTTTGATCGCCGAAGATCC
CCACCAATGCGTGAACGCAGGCACTAAATATTTGACTAAAACATGTGTTGATTGAATTTG
ATGAAGCAAGAGAAGAAACATTTTAACTTACTACACACATACAATGAAGATAAAATATAT
ATATCATTTTGCAAAAAAAGCAATTAATTTTAACACGGTTTTTTTGCTATTAATATTACT
ACTGATAAAATCAAATGACCAAAATTTTGTTTATTACAACTATATTTGTTTCGATGCTCA
TTTCTAATTATGCTGAAAATCTATTAAAAACTTAAATGTTTGAAATTATAAAAAAATTCT
AACAATGAATTATTGAATTTTTAAAAAATTTGTAACCACACACCAATTAGAATATTTCGA
ATTAATCATGTCCTTCTTTCAATTATTTTCTTTATTTTCTCTCACATATTAGTGTGTTCA
AAATTCTAATTTTTTCAATGTAAGAAGATGACGATTTTTATTAATAAAAAATCAAAACTA
AAAA
>g818.t17 Gene=g818 Length=268
MSRDNHLQRSRSRSLSRYRNYNSTSKSQRTTTPPQFSSSSSYRYNSRHESPPSKRSRYQK
ERSRSFEKNGSSGGRTRRRNSPATTDISRKNHEPSRVLGVFNLHVRTTEDEIREVFERFG
EIDNIVMVKDAKTRGFRGYCFLYYNKQRDATAALEECNGIEIKDRQIRVDYSLSEGPHVS
TPEYRGKRGRDNMRGQRPRHLSPLRGERTRYYDRYDNVRTRSRDRDRYDNDRFRRSPPRN
YDRSDYHRRGSPDRFDRRRSPPMRERRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g818.t17 | Coils | Coil | Coil | 268 | 268 | - |
| 5 | g818.t17 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 182 | 8.2E-27 |
| 12 | g818.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 92 | - |
| 8 | g818.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 47 | - |
| 10 | g818.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 48 | 74 | - |
| 11 | g818.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 173 | 268 | - |
| 9 | g818.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 181 | 260 | - |
| 2 | g818.t17 | PANTHER | PTHR15241 | TRANSFORMER-2-RELATED | 9 | 255 | 2.6E-21 |
| 3 | g818.t17 | PANTHER | PTHR15241:SF305 | - | 9 | 255 | 2.6E-21 |
| 1 | g818.t17 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 100 | 168 | 1.7E-18 |
| 13 | g818.t17 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 96 | 174 | 16.705 |
| 7 | g818.t17 | SMART | SM00360 | rrm1_1 | 97 | 170 | 3.6E-21 |
| 4 | g818.t17 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 89 | 199 | 2.96E-28 |
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 transcript has been annotated with K12897 (transformer-2 protein)
Pathway
- This transcript belongs to the following pathways
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. There were no conditions that were differentially expressed