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.t2 TTS g6156.t2 14630422 14630422
chr_2 g6156 g6156.t2 isoform g6156.t2 14630431 14632149
chr_2 g6156 g6156.t2 exon g6156.t2.exon1 14630431 14630577
chr_2 g6156 g6156.t2 exon g6156.t2.exon2 14630638 14630822
chr_2 g6156 g6156.t2 exon g6156.t2.exon3 14630915 14631067
chr_2 g6156 g6156.t2 exon g6156.t2.exon4 14631511 14631817
chr_2 g6156 g6156.t2 cds g6156.t2.CDS1 14631563 14631817
chr_2 g6156 g6156.t2 exon g6156.t2.exon5 14631884 14631982
chr_2 g6156 g6156.t2 cds g6156.t2.CDS2 14631884 14631982
chr_2 g6156 g6156.t2 exon g6156.t2.exon6 14632045 14632086
chr_2 g6156 g6156.t2 cds g6156.t2.CDS3 14632045 14632086
chr_2 g6156 g6156.t2 exon g6156.t2.exon7 14632147 14632149
chr_2 g6156 g6156.t2 cds g6156.t2.CDS4 14632147 14632149
chr_2 g6156 g6156.t2 TSS g6156.t2 14632224 14632224

Sequences

>g6156.t2 Gene=g6156 Length=936
ATGTTACCGCTATCACTATTAAAAACTGCTCAATCACACCCAATGCTTGTTGAGCTAAAG
AATGGTGAAACTTATAATGGACATCTTGTAAGTTGTGATACATGGATGAATATTAACTTA
CGAGAAGTTATTTGCACATCAAAGGATGGCGATAAGTTTTGGAGAATGAATGAATGCTAT
ATTCGTGGTAGCACAATCAAATATCTTCGTATTCCCGATGAAGTCATTGATTTAGTAAAA
GAAGACATTCAAGCTAAAGCAAAGAATCGTAATCAAAATCAGAACCAAAATCGTAACAAT
AACAACAACCAGCAAAATCGCGGAAATAAGAACAACCCAAACCAGCATCGTCCAAATCCA
AATCGTAATCGGAATAACGTCAATATCAATAAGAATTGATTATCTAGTGTATCTCTTTTT
AAGATGATAAGACTAAATTTATATTTTTCATCTTAAAATGAATCTGAACCCTATGTCAAA
AGCTATACAATCGTGTCGTTTTATGATAATGGCGCCAAAATGATTTTACAGCATGCGACA
AACTTGTTACACTATTGAATTACAGATAGTAAAGATGGGCGTTCTTCTTTAATGTACATG
ATAGACGTACTTTAAAAAATTCAACAATTAAGTATTTGAAAATGGATCCATGCAGTGACA
ACTCATGCAACAATAATGATGGTTCAATTAATTGCTGTCAAACCATTTGCAAACCAGTGA
TATGTGGCACAATAGGACCAAATAATGCTTGTTTTTACGATACCCCTTGTGTATTCTATC
AAGGATCTTATTCCAATGGAATTGCATACTTCTCATTATAAAATTATTGACATGAATGTT
CATTCAAGAGAGGAAGTTGCAAAAATCAACTATAAATCGGATGTTTTTTATTTTGACATA
ATTTTTTTCTGAATAAACATGAACATTATAAAAATT

>g6156.t2 Gene=g6156 Length=132
MLPLSLLKTAQSHPMLVELKNGETYNGHLVSCDTWMNINLREVICTSKDGDKFWRMNECY
IRGSTIKYLRIPDEVIDLVKEDIQAKAKNRNQNQNQNRNNNNNQQNRGNKNNPNQHRPNP
NRNRNNVNINKN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g6156.t2 CDD cd01723 LSm4 2 77 1.58003E-55
6 g6156.t2 Coils Coil Coil 84 104 -
5 g6156.t2 Gene3D G3DSA:2.30.30.100 - 1 83 2.8E-37
9 g6156.t2 MobiDBLite mobidb-lite consensus disorder prediction 86 132 -
10 g6156.t2 MobiDBLite mobidb-lite consensus disorder prediction 88 132 -
2 g6156.t2 PANTHER PTHR23338:SF16 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 1 123 3.0E-55
3 g6156.t2 PANTHER PTHR23338 SMALL NUCLEAR RIBONUCLEOPROTEIN SM 1 123 3.0E-55
1 g6156.t2 Pfam PF01423 LSM domain 6 69 8.1E-16
8 g6156.t2 SMART SM00651 Sm3 5 71 3.2E-18
4 g6156.t2 SUPERFAMILY SSF50182 Sm-like ribonucleoproteins 3 118 3.78E-31

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

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