Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Probable small nuclear ribonucleoprotein Sm D2.

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_2 g8195 g8195.t4 TSS g8195.t4 29032379 29032379
chr_2 g8195 g8195.t4 isoform g8195.t4 29032444 29032915
chr_2 g8195 g8195.t4 exon g8195.t4.exon1 29032444 29032451
chr_2 g8195 g8195.t4 exon g8195.t4.exon2 29032554 29032915
chr_2 g8195 g8195.t4 cds g8195.t4.CDS1 29032562 29032915
chr_2 g8195 g8195.t4 TTS g8195.t4 29032937 29032937

Sequences

>g8195.t4 Gene=g8195 Length=370
ATGTGTAACGCTTGCTATGAAGCCGAAATCTGAAATGACACCAGAAGAGTTACAAAAGCT
TGAAGAAGAAGAATTTAATACGGGACCATTAAGTGTTCTTACTCAATCTGTCAAAAACAA
CACTCAAGTTTTAATTAATTGCAGAAACAACAAGAAACTTCTTGGTCGTGTTAAAGCATT
TGATCGTCATTGTAATATGGTATTGGAAAATGTTAAAGAAATGTGGACAGAAGTTCCAAA
AAGCGGTAAAGGAAAAAAAAAAGTTAAACCAGTTAGTAAAGATAGATACATCAGTAAAAT
GTTCTTACGAGGAGATTCTGTTGTTCTTGTGCTTAGAAATCCACTCGCTGCTCAAGCTGC
AACAAAATAA

>g8195.t4 Gene=g8195 Length=117
MKPKSEMTPEELQKLEEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCN
MVLENVKEMWTEVPKSGKGKKKVKPVSKDRYISKMFLRGDSVVLVLRNPLAAQAATK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g8195.t4 CDD cd01720 Sm_D2 20 109 4.08599E-53
7 g8195.t4 Gene3D G3DSA:2.30.30.100 - 1 111 1.3E-41
5 g8195.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
6 g8195.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 18 -
2 g8195.t4 PANTHER PTHR12777 SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2 2 109 9.4E-59
1 g8195.t4 Pfam PF01423 LSM domain 33 105 2.7E-19
4 g8195.t4 SMART SM00651 Sm3 28 107 4.1E-19
3 g8195.t4 SUPERFAMILY SSF50182 Sm-like ribonucleoproteins 23 108 4.5E-26

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:0030532 small nuclear ribonucleoprotein complex CC
GO:0008380 RNA splicing BP

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