Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm7.

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 g4554 g4554.t5 TTS g4554.t5 3229343 3229343
chr_2 g4554 g4554.t5 isoform g4554.t5 3229443 3229895
chr_2 g4554 g4554.t5 exon g4554.t5.exon1 3229443 3229573
chr_2 g4554 g4554.t5 cds g4554.t5.CDS1 3229443 3229573
chr_2 g4554 g4554.t5 exon g4554.t5.exon2 3229641 3229723
chr_2 g4554 g4554.t5 cds g4554.t5.CDS2 3229641 3229723
chr_2 g4554 g4554.t5 exon g4554.t5.exon3 3229786 3229895
chr_2 g4554 g4554.t5 cds g4554.t5.CDS3 3229786 3229895
chr_2 g4554 g4554.t5 TSS g4554.t5 3229969 3229969

Sequences

>g4554.t5 Gene=g4554 Length=324
ATGGCTGATAAGAAGCAAAATGATAATAAAAATGAAAAGAAGAGGAAAGAGAGTATTTTA
GATTTATCTAAGTATCTTGAAAAACAGATCCGTGTAAAGTTTGCCGGTTTAGAATGTTCA
GGCATTTTAAAAGGCTTTGATCCACTTCTAAATTTGGTACTTGATAATACCACAGAGTAT
TTAAGAGATCCAGATGAACCCTACAAGTTTTCAGAAGATACCCGAAACTTGGGATTGGTA
GTCTGTAGAGGAACATCTGTTGTATTAATATGTCCACAAGATGGCATGGAAGCCATTTCA
AACCCATTTCTACCACAAGATTAA

>g4554.t5 Gene=g4554 Length=107
MADKKQNDNKNEKKRKESILDLSKYLEKQIRVKFAGLECSGILKGFDPLLNLVLDNTTEY
LRDPDEPYKFSEDTRNLGLVVCRGTSVVLICPQDGMEAISNPFLPQD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g4554.t5 CDD cd01729 LSm7 16 103 0
6 g4554.t5 Gene3D G3DSA:2.30.30.100 - 1 101 0
2 g4554.t5 PANTHER PTHR10553 SMALL NUCLEAR RIBONUCLEOPROTEIN 2 106 0
3 g4554.t5 PANTHER PTHR10553:SF5 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7 2 106 0
7 g4554.t5 PIRSF PIRSF037188 Lsm7 1 107 0
1 g4554.t5 Pfam PF01423 LSM domain 21 92 0
5 g4554.t5 SMART SM00651 Sm3 20 92 0
4 g4554.t5 SUPERFAMILY SSF50182 Sm-like ribonucleoproteins 22 96 0

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: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. There were no conditions that were differentially expressed