General information for g818.t15
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.t15 | TSS | g818.t15 | 6163279 | 6163279 |
| chr_3 | g818 | g818.t15 | isoform | g818.t15 | 6163399 | 6165060 |
| chr_3 | g818 | g818.t15 | exon | g818.t15.exon1 | 6163399 | 6163418 |
| chr_3 | g818 | g818.t15 | cds | g818.t15.CDS1 | 6163399 | 6163418 |
| chr_3 | g818 | g818.t15 | exon | g818.t15.exon2 | 6163538 | 6163582 |
| chr_3 | g818 | g818.t15 | cds | g818.t15.CDS2 | 6163538 | 6163582 |
| chr_3 | g818 | g818.t15 | exon | g818.t15.exon3 | 6163672 | 6163879 |
| chr_3 | g818 | g818.t15 | cds | g818.t15.CDS3 | 6163672 | 6163879 |
| chr_3 | g818 | g818.t15 | exon | g818.t15.exon4 | 6163984 | 6164254 |
| chr_3 | g818 | g818.t15 | cds | g818.t15.CDS4 | 6163984 | 6164254 |
| chr_3 | g818 | g818.t15 | exon | g818.t15.exon5 | 6164338 | 6165060 |
| chr_3 | g818 | g818.t15 | cds | g818.t15.CDS5 | 6164338 | 6164603 |
| chr_3 | g818 | g818.t15 | TTS | g818.t15 | 6165054 | 6165054 |
Sequences
>g818.t15 Gene=g818 Length=1267
ATGTCGCGCGACAATCATTTACAAAGATCGAGAAGCCGCTCACTTTCCAGATACCGCAAT
TACAATACCTCGAAATCACAACGAACAACCACACCACCGCAATTTTCATCATCATCGTCC
TACAGATATAATTCTCGCCATGAGTCACCACCATCAAAGCGATCGAGATATCAAAAGGAA
CGCAGTCGTTCGTTTGAAAAGAATGGAAGCAGCGGTGGACGAACCAGAAGACGCAATTCA
CCAGCGACAACCGATATAAGTCGTAAAAATCATGAGCCCTCTAGAGTTTTGGGCGTCTTT
AATTTGCATGTTCGCACGACTGAGGATGAAATTCGTGAAGTTTTCGAACGTTTTGGAGAA
ATTGACAATATTGTTATGGTAAAAGATGCAAAAACAAGAGGATTTCGAGGCTATTGCTTT
TTGTATTACAATAAGCAACGAGATGCAACAGCTGCCTTAGAGGAATGCAATGGTATAGAG
ATCAAAGATCGGCAAATTCGCGTAGATTATTCATTAAGTGAAGGTCCTCATGTGAGCACT
CCAGCAGGAGAATATCGAGGAAAACGGGGAAGAGATAATATGCGCGGCCAAAGACCACGT
CATTTAAGTCCATTGCGTGGAGAGAGAACTCGTTATTACGATAGATATGACAATGTTCGA
ACTCGCTCGCGTGATAGAGACAGATATGACAACGATCGTTTTAGACGTTCACCGCCTCGT
AATTATGATAGATCTGATTATCATCGTCGTGGATCACCTGATCGCTTTGATCGCCGAAGA
TCCCCACCAATGCGTGAACGCAGGCACTAAATATTTGACTAAAACATGTGTTGATTGAAT
TTGATGAAGCAAGAGAAGAAACATTTTAACTTACTACACACATACAATGAAGATAAAATA
TATATATCATTTTGCAAAAAAAGCAATTAATTTTAACACGGTTTTTTTGCTATTAATATT
ACTACTGATAAAATCAAATGACCAAAATTTTGTTTATTACAACTATATTTGTTTCGATGC
TCATTTCTAATTATGCTGAAAATCTATTAAAAACTTAAATGTTTGAAATTATAAAAAAAT
TCTAACAATGAATTATTGAATTTTTAAAAAATTTGTAACCACACACCAATTAGAATATTT
CGAATTAATCATGTCCTTCTTTCAATTATTTTCTTTATTTTCTCTCACATATTAGTGTGT
TCAAAATTCTAATTTTTTCAATGTAAGAAGATGACGATTTTTATTAATAAAAAATCAAAA
CTAAAAA
>g818.t15 Gene=g818 Length=269
MSRDNHLQRSRSRSLSRYRNYNTSKSQRTTTPPQFSSSSSYRYNSRHESPPSKRSRYQKE
RSRSFEKNGSSGGRTRRRNSPATTDISRKNHEPSRVLGVFNLHVRTTEDEIREVFERFGE
IDNIVMVKDAKTRGFRGYCFLYYNKQRDATAALEECNGIEIKDRQIRVDYSLSEGPHVST
PAGEYRGKRGRDNMRGQRPRHLSPLRGERTRYYDRYDNVRTRSRDRDRYDNDRFRRSPPR
NYDRSDYHRRGSPDRFDRRRSPPMRERRH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g818.t15 | Gene3D | G3DSA:3.30.70.330 | - | 2 | 180 | 5.7E-27 |
| 9 | g818.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 91 | - |
| 7 | g818.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 14 | 46 | - |
| 8 | g818.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 47 | 73 | - |
| 6 | g818.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 172 | 269 | - |
| 10 | g818.t15 | MobiDBLite | mobidb-lite | consensus disorder prediction | 184 | 261 | - |
| 2 | g818.t15 | PANTHER | PTHR15241 | TRANSFORMER-2-RELATED | 9 | 256 | 2.7E-23 |
| 3 | g818.t15 | PANTHER | PTHR15241:SF305 | - | 9 | 256 | 2.7E-23 |
| 1 | g818.t15 | Pfam | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 99 | 167 | 1.7E-18 |
| 12 | g818.t15 | ProSiteProfiles | PS50102 | Eukaryotic RNA Recognition Motif (RRM) profile. | 95 | 173 | 16.705 |
| 5 | g818.t15 | SMART | SM00360 | rrm1_1 | 96 | 169 | 3.6E-21 |
| 4 | g818.t15 | SUPERFAMILY | SSF54928 | RNA-binding domain, RBD | 88 | 197 | 1.17E-27 |
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.
