General information for g4539.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lipase 1.
Parent gene
- The parent gene g4539 is located on chr_2: 3173370..3174773 (- 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 | g4539 | g4539.t1 | isoform | g4539.t1 | 3173370 | 3174773 |
| chr_2 | g4539 | g4539.t1 | exon | g4539.t1.exon1 | 3173370 | 3173513 |
| chr_2 | g4539 | g4539.t1 | cds | g4539.t1.CDS1 | 3173370 | 3173513 |
| chr_2 | g4539 | g4539.t1 | exon | g4539.t1.exon2 | 3173597 | 3174136 |
| chr_2 | g4539 | g4539.t1 | cds | g4539.t1.CDS2 | 3173597 | 3174136 |
| chr_2 | g4539 | g4539.t1 | exon | g4539.t1.exon3 | 3174216 | 3174773 |
| chr_2 | g4539 | g4539.t1 | cds | g4539.t1.CDS3 | 3174216 | 3174773 |
| chr_2 | g4539 | g4539.t1 | TSS | g4539.t1 | NA | NA |
| chr_2 | g4539 | g4539.t1 | TTS | g4539.t1 | NA | NA |
Sequences
>g4539.t1 Gene=g4539 Length=1242
ATGCTTAGTCTCATTGCAGTACTTGGGGAAGCAAGTAGTAAAAAACAGCTCGATAGAGCA
AAAAAAATATTATCTAAGAAAAATATGGAAATTTTATTCGTGGCTGTAGTGATATCTAAA
GTTGTAACTTTCGCGAATGCCAAAGATGATGATATTTTAAAAATCGTATCAAAAGCTGGA
TTTTCGGGTGAATTTAATGAAATCAACACAGAAGATGACTACATCCTTGGCGTCCATAAA
ATTAATTCAAAAATCGCAAATACAACAAAGTATCCAATATTTATTATGCACGGCTTTCTA
ACAACTCCAATGAGTTTTTTCTTAACTGGTCAAAAAAATTCACTGCCATTAATTTTAGCC
GATAATGGACACGATGTCTTTCTCGGATCGCGAAGAGGTTCAAAATATTCGTCAAAGCAT
TTACATTTATCAATAGAATCACGAGATTTTTGGGATTTTACTTGGCATGAAATTGGATAT
TATGATCTTAAAGCGATCATTGACTTTATTCTTGAAAACACGAATGCCAATAAAATATTC
TTCGTGGGCTATTCGCAGGGAAACACGGAACTGCTTGTTTTACTGTCGATGCGACCACAA
TATAACGAAGTCATAGATCAAGCACATTTAATGTCATGTGTTGGTGCAATAACAAATGTC
CATGAACTTGGCAGCCTTTTAAGTCCATTGCTGTTGAACTATGCTAAAACACATGATGAT
TTTTACTATTTAAATATGCAGTCACTTATACCACTGCAAGTCGAATTAGCTAAAATACTC
TGTAGCTCATTGCGCCAAATTCGAGTCGCATTGTGTAAGAACATAATATTTTTCATGGTT
GGTCGCAATCATCGTTCGACGGAAGTCGATCCACAGACCTATGCTAAAATGTTCGAACAA
CTGTCGCCCATAGTTGGAGTGAAACAACTCTTGCACTTTGCACAGTTAATAATGACATCA
AAATTTCAACAGTTTGACTATGGACGTAGAAATATCGAGATTTACAACTCAACTACTCCA
CCTCAGTACGATTTAGCAAAAATTACAGCACCAATTTATCTTTACATTGGGGAAGAAGAT
ATCATTTTTAACCGAAAAGATTCAGACAAGCTTGCCAAAATATTGCCAAATGTTGTAGCC
AAAAAGATGATAAGAAATTATAATCATTTCGATTTTGTTTATGGTCGAAATTCACATAAA
TTATTGTATAAACAAATTTTAGAATTTATTGAGACAATTTGA
>g4539.t1 Gene=g4539 Length=413
MLSLIAVLGEASSKKQLDRAKKILSKKNMEILFVAVVISKVVTFANAKDDDILKIVSKAG
FSGEFNEINTEDDYILGVHKINSKIANTTKYPIFIMHGFLTTPMSFFLTGQKNSLPLILA
DNGHDVFLGSRRGSKYSSKHLHLSIESRDFWDFTWHEIGYYDLKAIIDFILENTNANKIF
FVGYSQGNTELLVLLSMRPQYNEVIDQAHLMSCVGAITNVHELGSLLSPLLLNYAKTHDD
FYYLNMQSLIPLQVELAKILCSSLRQIRVALCKNIIFFMVGRNHRSTEVDPQTYAKMFEQ
LSPIVGVKQLLHFAQLIMTSKFQQFDYGRRNIEIYNSTTPPQYDLAKITAPIYLYIGEED
IIFNRKDSDKLAKILPNVVAKKMIRNYNHFDFVYGRNSHKLLYKQILEFIETI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g4539.t1 | Gene3D | G3DSA:3.40.50.1820 | - | 41 | 412 | 1.3E-101 |
| 2 | g4539.t1 | PANTHER | PTHR11005:SF127 | LIPASE-RELATED | 31 | 411 | 1.2E-95 |
| 3 | g4539.t1 | PANTHER | PTHR11005 | LYSOSOMAL ACID LIPASE-RELATED | 31 | 411 | 1.2E-95 |
| 11 | g4539.t1 | PIRSF | PIRSF000862 | Steryl_ester_lip | 4 | 413 | 3.4E-92 |
| 1 | g4539.t1 | Pfam | PF00561 | alpha/beta hydrolase fold | 92 | 394 | 5.5E-16 |
| 7 | g4539.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 13 | - |
| 8 | g4539.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 9 | g4539.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 9 | - |
| 10 | g4539.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 10 | 13 | - |
| 6 | g4539.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 14 | 413 | - |
| 4 | g4539.t1 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 51 | 411 | 1.21E-45 |
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:0016788 | hydrolase activity, acting on ester bonds | MF |
KEGG
Orthology
- This transcript has been annotated with K01052 (lysosomal acid lipase/cholesteryl ester hydrolase)
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. There were no conditions that were differentially expressed