Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm4.

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 g6156 g6156.t4 TTS g6156.t4 14631460 14631460
chr_2 g6156 g6156.t4 isoform g6156.t4 14631563 14632149
chr_2 g6156 g6156.t4 exon g6156.t4.exon1 14631563 14631817
chr_2 g6156 g6156.t4 cds g6156.t4.CDS1 14631563 14631817
chr_2 g6156 g6156.t4 exon g6156.t4.exon2 14631884 14631982
chr_2 g6156 g6156.t4 cds g6156.t4.CDS2 14631884 14631982
chr_2 g6156 g6156.t4 exon g6156.t4.exon3 14632045 14632149
chr_2 g6156 g6156.t4 cds g6156.t4.CDS3 14632045 14632047
chr_2 g6156 g6156.t4 TSS g6156.t4 14632224 14632224

Sequences

>g6156.t4 Gene=g6156 Length=459
ATGGTAAGAATAAGAGTTAAAATTGTTCCTATTCAATGACTCATTCATTTATTTATCTTT
TAGTTACCGCTATCACTATTAAAAACTGCTCAATCACACCCAATGCTTGTTGAGCTAAAG
AATGGTGAAACTTATAATGGACATCTTGTAAGTTGTGATACATGGATGAATATTAACTTA
CGAGAAGTTATTTGCACATCAAAGGATGGCGATAAGTTTTGGAGAATGAATGAATGCTAT
ATTCGTGGTAGCACAATCAAATATCTTCGTATTCCCGATGAAGTCATTGATTTAGTAAAA
GAAGACATTCAAGCTAAAGCAAAGAATCGTAATCAAAATCAGAACCAAAATCGTAACAAT
AACAACAACCAGCAAAATCGCGGAAATAAGAACAACCCAAACCAGCATCGTCCAAATCCA
AATCGTAATCGGAATAACGTCAATATCAATAAGAATTGA

>g6156.t4 Gene=g6156 Length=118
MLVELKNGETYNGHLVSCDTWMNINLREVICTSKDGDKFWRMNECYIRGSTIKYLRIPDE
VIDLVKEDIQAKAKNRNQNQNQNRNNNNNQQNRGNKNNPNQHRPNPNRNRNNVNINKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6156.t4 CDD cd01723 LSm4 1 63 1.40972E-45
6 g6156.t4 Coils Coil Coil 70 90 -
5 g6156.t4 Gene3D G3DSA:2.30.30.100 - 1 69 4.8E-31
10 g6156.t4 MobiDBLite mobidb-lite consensus disorder prediction 72 118 -
9 g6156.t4 MobiDBLite mobidb-lite consensus disorder prediction 74 118 -
2 g6156.t4 PANTHER PTHR23338:SF16 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 1 109 3.6E-45
3 g6156.t4 PANTHER PTHR23338 SMALL NUCLEAR RIBONUCLEOPROTEIN SM 1 109 3.6E-45
1 g6156.t4 Pfam PF01423 LSM domain 1 55 9.9E-14
8 g6156.t4 SMART SM00651 Sm3 1 57 1.3E-9
4 g6156.t4 SUPERFAMILY SSF50182 Sm-like ribonucleoproteins 1 104 2.77E-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:0006396 RNA processing BP
GO:0000398 mRNA splicing, via spliceosome BP
GO:0000956 nuclear-transcribed mRNA catabolic process BP

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.

Raw TPM values