General information for g12349.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lipase 3.
Parent gene
- The parent gene g12349 is located on chr_1: 22723566..22724299 (+ 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_1 | g12349 | g12349.t1 | TSS | g12349.t1 | 22722897 | 22722897 |
| chr_1 | g12349 | g12349.t1 | isoform | g12349.t1 | 22722938 | 22724299 |
| chr_1 | g12349 | g12349.t1 | exon | g12349.t1.exon1 | 22722938 | 22723024 |
| chr_1 | g12349 | g12349.t1 | cds | g12349.t1.CDS1 | 22722938 | 22723024 |
| chr_1 | g12349 | g12349.t1 | exon | g12349.t1.exon2 | 22723083 | 22723482 |
| chr_1 | g12349 | g12349.t1 | cds | g12349.t1.CDS2 | 22723083 | 22723482 |
| chr_1 | g12349 | g12349.t1 | exon | g12349.t1.exon3 | 22723538 | 22723913 |
| chr_1 | g12349 | g12349.t1 | cds | g12349.t1.CDS3 | 22723538 | 22723913 |
| chr_1 | g12349 | g12349.t1 | exon | g12349.t1.exon4 | 22723969 | 22724299 |
| chr_1 | g12349 | g12349.t1 | cds | g12349.t1.CDS4 | 22723969 | 22724299 |
| chr_1 | g12349 | g12349.t1 | TTS | g12349.t1 | 22724340 | 22724340 |
Sequences
>g12349.t1 Gene=g12349 Length=1194
ATGAAAACTGCACAAATTTTAATTGTTTTTTTGGCATTATTTTCTGTTGTGTTTGCTGAT
GTTTGGGAAGATACACAATTAAATACAATTCAACTTTTAAGAAAGTATGGCTATACAGCA
GAAGAATATTCAGTAACAACATCAGATGGTTATCGATTAGGTATTCATCGTTGTTCTGGT
GGTCCAGTTTCACCACCAGCTGCTAATAAGCCAGTAGCATTTCTTATGCATGGACAACTT
AGTTCATCTGCTGATTATGTAATTATGGGTCCACAAGTTTCACTAGCTTATATGCTATCT
GATCTTGGTTATGATGTATGGATGGGAAATTCACATGGAAATAGATATTCAAATACTCAT
ACATCACTTAATAATGAAACAAAAGCTTATTGGGATTTTTCATGGCATGAAATAGGTTCA
ATTGATGTTCCTACAATGATTGACTATATTTTAGCGAGAACAGGACAAAGAAATTTGCAT
TATATTGGTCATTCAATGGGAACAACAGTTTATTTTGTAATGATTAGTGAAAAACCAGCT
TATGCTTCTAAACTAAGAAGTGTCAATTTGTTAGCTCCTGCAACTTATATGACATATATT
GTAACACCTTATGTTCGTTGGATTGCTGCTTATGCTTATACATGGGATTTAATGTTCAAT
ATGATGGGAACATACTATTTTGCACCAACTGATGAGATGGACAAACAAGCTGCTTATAAT
GATTGTCGTGATGGTGCACCTTATCAAGAAATGTGCGCAATACAAATTTTCCTTATCGCT
GGATGGAATTCTCAAGAAACAAATCGAACAATGTTGCCAGTTATGAATGCACATTCACCT
GCTGGAGCAAGCATGATGAATATGTTGCATTATGCTCAAATAGTAAGAAGTGGAATTTTC
CAACAATATGATCATGGTGTCAATAATATCTACAGATATGGTCAATTAACACCTCCATTA
TATAGATTCACTGGTCATACTGCACCATTACATTTATTTTGGTCAACAAATGATTGGATG
GCAACACCAGCTGATGTATCGACACTTTATAATCGATTAGGTGGTTCAAGTGTTGTAGAT
TTATTTTATCATGTACCACAAGTTGAATGGAATCATATGGACTTTGTTTGGGGTATTAAT
GTTAGACGTTTGGTTTATAACAGAATGGTTGAAGAAATGAGAAAATATGACTGA
>g12349.t1 Gene=g12349 Length=397
MKTAQILIVFLALFSVVFADVWEDTQLNTIQLLRKYGYTAEEYSVTTSDGYRLGIHRCSG
GPVSPPAANKPVAFLMHGQLSSSADYVIMGPQVSLAYMLSDLGYDVWMGNSHGNRYSNTH
TSLNNETKAYWDFSWHEIGSIDVPTMIDYILARTGQRNLHYIGHSMGTTVYFVMISEKPA
YASKLRSVNLLAPATYMTYIVTPYVRWIAAYAYTWDLMFNMMGTYYFAPTDEMDKQAAYN
DCRDGAPYQEMCAIQIFLIAGWNSQETNRTMLPVMNAHSPAGASMMNMLHYAQIVRSGIF
QQYDHGVNNIYRYGQLTPPLYRFTGHTAPLHLFWSTNDWMATPADVSTLYNRLGGSSVVD
LFYHVPQVEWNHMDFVWGINVRRLVYNRMVEEMRKYD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g12349.t1 | Gene3D | G3DSA:3.40.50.1820 | - | 18 | 395 | 4.2E-126 |
| 3 | g12349.t1 | PANTHER | PTHR11005:SF127 | LIPASE-RELATED | 5 | 396 | 4.8E-130 |
| 4 | g12349.t1 | PANTHER | PTHR11005 | LYSOSOMAL ACID LIPASE-RELATED | 5 | 396 | 4.8E-130 |
| 13 | g12349.t1 | PIRSF | PIRSF000862 | Steryl_ester_lip | 3 | 397 | 5.1E-121 |
| 2 | g12349.t1 | Pfam | PF04083 | Partial alpha/beta-hydrolase lipase region | 31 | 89 | 2.2E-17 |
| 1 | g12349.t1 | Pfam | PF00561 | alpha/beta hydrolase fold | 92 | 350 | 2.2E-16 |
| 9 | g12349.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 10 | g12349.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 11 | g12349.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 12 | g12349.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 8 | g12349.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 397 | - |
| 5 | g12349.t1 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 24 | 393 | 5.61E-53 |
| 6 | g12349.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
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 |
| GO:0006629 | lipid metabolic process | BP |
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