General information for g4554.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U6 snRNA-associated Sm-like protein LSm7.
Parent gene
- The parent gene g4554 is located on chr_2: 3229443..3233549 (- strand)
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.t7 | TTS | g4554.t7 | 3229343 | 3229343 |
| chr_2 | g4554 | g4554.t7 | isoform | g4554.t7 | 3229443 | 3233549 |
| chr_2 | g4554 | g4554.t7 | exon | g4554.t7.exon1 | 3229443 | 3229573 |
| chr_2 | g4554 | g4554.t7 | cds | g4554.t7.CDS1 | 3229443 | 3229573 |
| chr_2 | g4554 | g4554.t7 | exon | g4554.t7.exon2 | 3229641 | 3229730 |
| chr_2 | g4554 | g4554.t7 | cds | g4554.t7.CDS2 | 3229641 | 3229730 |
| chr_2 | g4554 | g4554.t7 | exon | g4554.t7.exon3 | 3229790 | 3229903 |
| chr_2 | g4554 | g4554.t7 | cds | g4554.t7.CDS3 | 3229790 | 3229895 |
| chr_2 | g4554 | g4554.t7 | TSS | g4554.t7 | 3229969 | 3229969 |
| chr_2 | g4554 | g4554.t7 | exon | g4554.t7.exon4 | 3233110 | 3233549 |
Sequences
>g4554.t7 Gene=g4554 Length=775
TTGGTACATTTGTAGTACTATAATTTTTTGAATAATCCGTGTTGAAATAATACTTATTTT
TCCATAAGAACCACGATAAGATTATCACGAAAAAAGCAAAAAAATAAATAAACATTTTCG
TTTGTTGTGCACTCTACTACTGCCGATGACAACTGAAAATGAGTGATAACTCTCTGAGCA
TTTATATGAAAATACTTCCATTTACTAATCTCTGTGATTGTGAGAGAACTTTGCGCGATT
TTTTTTATTGACACTTTATTCTTATCAAAAACCCTAAAAAGGTATAAAATTTCGTCAAAC
ATGCACACAAAACAAAAATTTTTAATATAAATTTAATGTGGTTGAATTCATTTAAATAAA
AGCAAATATTTAAGTTGTAAAATTATTAGAAATAGTCATAGCCAAGGTTAACATAGAGAT
ATATCATTATTTTTTGCAAGGTCAAAATATGGCTGATAAGAAGCAAAATGATAATAAAAA
TGAAAAGAAGAGGAAAGAGAGTATTTTAGATTTATCTAAGTATCTTGAAAAACAGATCCG
TGTAAAGTTTGCCGGTGGTAGAGAATGTTCAGGCATTTTAAAAGGCTTTGATCCACTTCT
AAATTTGGTACTTGATAATACCACAGAGTATTTAAGAGATCCAGATGAACCCTACAAGTT
TTCAGAAGATACCCGAAACTTGGGATTGGTAGTCTGTAGAGGAACATCTGTTGTATTAAT
ATGTCCACAAGATGGCATGGAAGCCATTTCAAACCCATTTCTACCACAAGATTAA
>g4554.t7 Gene=g4554 Length=108
MADKKQNDNKNEKKRKESILDLSKYLEKQIRVKFAGGRECSGILKGFDPLLNLVLDNTTE
YLRDPDEPYKFSEDTRNLGLVVCRGTSVVLICPQDGMEAISNPFLPQD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4554.t7 | CDD | cd01729 | LSm7 | 16 | 104 | 0 |
| 6 | g4554.t7 | Gene3D | G3DSA:2.30.30.100 | - | 1 | 102 | 0 |
| 2 | g4554.t7 | PANTHER | PTHR10553 | SMALL NUCLEAR RIBONUCLEOPROTEIN | 2 | 107 | 0 |
| 3 | g4554.t7 | PANTHER | PTHR10553:SF5 | U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM7 | 2 | 107 | 0 |
| 7 | g4554.t7 | PIRSF | PIRSF037188 | Lsm7 | 1 | 108 | 0 |
| 1 | g4554.t7 | Pfam | PF01423 | LSM domain | 21 | 93 | 0 |
| 5 | g4554.t7 | SMART | SM00651 | Sm3 | 20 | 93 | 0 |
| 4 | g4554.t7 | SUPERFAMILY | SSF50182 | Sm-like ribonucleoproteins | 22 | 97 | 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 transcript has been annotated with K12626 (U6 snRNA-associated Sm-like protein LSm7)
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.
