Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Transformer-2 sex-determining protein.

Parent gene

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.t2 TSS g818.t2 6163279 6163279
chr_3 g818 g818.t2 isoform g818.t2 6163399 6164603
chr_3 g818 g818.t2 exon g818.t2.exon1 6163399 6163418
chr_3 g818 g818.t2 cds g818.t2.CDS1 6163399 6163418
chr_3 g818 g818.t2 exon g818.t2.exon2 6163538 6163582
chr_3 g818 g818.t2 cds g818.t2.CDS2 6163538 6163582
chr_3 g818 g818.t2 exon g818.t2.exon3 6163669 6163879
chr_3 g818 g818.t2 cds g818.t2.CDS3 6163669 6163879
chr_3 g818 g818.t2 exon g818.t2.exon4 6163984 6164254
chr_3 g818 g818.t2 cds g818.t2.CDS4 6163984 6164254
chr_3 g818 g818.t2 exon g818.t2.exon5 6164338 6164603
chr_3 g818 g818.t2 cds g818.t2.CDS5 6164338 6164603
chr_3 g818 g818.t2 TTS g818.t2 6165054 6165054

Sequences

>g818.t2 Gene=g818 Length=813
ATGTCGCGCGACAATCATTTACAAAGATCGAGAAGCCGCTCACTTTCCAGATACCGCAAT
TACAACAGTACCTCGAAATCACAACGAACAACCACACCACCGCAATTTTCATCATCATCG
TCCTACAGATATAATTCTCGCCATGAGTCACCACCATCAAAGCGATCGAGATATCAAAAG
GAACGCAGTCGTTCGTTTGAAAAGAATGGAAGCAGCGGTGGACGAACCAGAAGACGCAAT
TCACCAGCGACAACCGATATAAGTCGTAAAAATCATGAGCCCTCTAGAGTTTTGGGCGTC
TTTAATTTGCATGTTCGCACGACTGAGGATGAAATTCGTGAAGTTTTCGAACGTTTTGGA
GAAATTGACAATATTGTTATGGTAAAAGATGCAAAAACAAGAGGATTTCGAGGCTATTGC
TTTTTGTATTACAATAAGCAACGAGATGCAACAGCTGCCTTAGAGGAATGCAATGGTATA
GAGATCAAAGATCGGCAAATTCGCGTAGATTATTCATTAAGTGAAGGTCCTCATGTGAGC
ACTCCAGCAGGAGAATATCGAGGAAAACGGGGAAGAGATAATATGCGCGGCCAAAGACCA
CGTCATTTAAGTCCATTGCGTGGAGAGAGAACTCGTTATTACGATAGATATGACAATGTT
CGAACTCGCTCGCGTGATAGAGACAGATATGACAACGATCGTTTTAGACGTTCACCGCCT
CGTAATTATGATAGATCTGATTATCATCGTCGTGGATCACCTGATCGCTTTGATCGCCGA
AGATCCCCACCAATGCGTGAACGCAGGCACTAA

>g818.t2 Gene=g818 Length=270
MSRDNHLQRSRSRSLSRYRNYNSTSKSQRTTTPPQFSSSSSYRYNSRHESPPSKRSRYQK
ERSRSFEKNGSSGGRTRRRNSPATTDISRKNHEPSRVLGVFNLHVRTTEDEIREVFERFG
EIDNIVMVKDAKTRGFRGYCFLYYNKQRDATAALEECNGIEIKDRQIRVDYSLSEGPHVS
TPAGEYRGKRGRDNMRGQRPRHLSPLRGERTRYYDRYDNVRTRSRDRDRYDNDRFRRSPP
RNYDRSDYHRRGSPDRFDRRRSPPMRERRH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g818.t2 Gene3D G3DSA:3.30.70.330 - 2 181 8.9E-27
10 g818.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 92 -
6 g818.t2 MobiDBLite mobidb-lite consensus disorder prediction 14 47 -
8 g818.t2 MobiDBLite mobidb-lite consensus disorder prediction 48 74 -
9 g818.t2 MobiDBLite mobidb-lite consensus disorder prediction 173 270 -
7 g818.t2 MobiDBLite mobidb-lite consensus disorder prediction 185 262 -
2 g818.t2 PANTHER PTHR15241 TRANSFORMER-2-RELATED 9 257 8.8E-22
3 g818.t2 PANTHER PTHR15241:SF305 - 9 257 8.8E-22
1 g818.t2 Pfam PF00076 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 100 168 1.7E-18
12 g818.t2 ProSiteProfiles PS50102 Eukaryotic RNA Recognition Motif (RRM) profile. 96 174 16.705
5 g818.t2 SMART SM00360 rrm1_1 97 170 3.6E-21
4 g818.t2 SUPERFAMILY SSF54928 RNA-binding domain, RBD 89 198 1.26E-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

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.

Raw TPM values