General information for g4538.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lipase 3.
Parent gene
- The parent gene g4538 is located on chr_2: 3171016..3173007 (- 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 | g4538 | g4538.t1 | isoform | g4538.t1 | 3171016 | 3173007 |
| chr_2 | g4538 | g4538.t1 | exon | g4538.t1.exon1 | 3171016 | 3171165 |
| chr_2 | g4538 | g4538.t1 | cds | g4538.t1.CDS1 | 3171016 | 3171165 |
| chr_2 | g4538 | g4538.t1 | exon | g4538.t1.exon2 | 3171661 | 3171885 |
| chr_2 | g4538 | g4538.t1 | cds | g4538.t1.CDS2 | 3171661 | 3171885 |
| chr_2 | g4538 | g4538.t1 | exon | g4538.t1.exon3 | 3171946 | 3172119 |
| chr_2 | g4538 | g4538.t1 | cds | g4538.t1.CDS3 | 3171946 | 3172119 |
| chr_2 | g4538 | g4538.t1 | exon | g4538.t1.exon4 | 3172271 | 3172584 |
| chr_2 | g4538 | g4538.t1 | cds | g4538.t1.CDS4 | 3172271 | 3172584 |
| chr_2 | g4538 | g4538.t1 | exon | g4538.t1.exon5 | 3172695 | 3173007 |
| chr_2 | g4538 | g4538.t1 | cds | g4538.t1.CDS5 | 3172695 | 3173007 |
| chr_2 | g4538 | g4538.t1 | TSS | g4538.t1 | 3173045 | 3173045 |
| chr_2 | g4538 | g4538.t1 | TTS | g4538.t1 | NA | NA |
Sequences
>g4538.t1 Gene=g4538 Length=1176
ATGAAACTCAATTCTCGATTTGTCGTGTTGATTTTATATTATTGTGTCACTTTAACTTTA
CAAGACAATCCTGAAGGCGATCAAGTACTTCAGTTAATCTCAAGTGCTGGCTTCCAAGGA
GAAGCGCACTACACAGAAACAGATGATGGATATGAATTGAAAATACATCGAATAGTGCCC
AAAATTCATAATGGTCGTGAACCTGTAATTTTAATGCATGGTCTTTTAGCGACAGCTGCT
GATTTTTTAATTACTGGACCTGATATTGCAATTGCTTATTTACTGTCGAATAATGGCTAT
GACGTCTATCTTGGTAATTCCCGAGGAAATAAATATTCAACAAAGCACCGCATTTACACA
ACGGATTCAACAGAATATTGGCGTTATAGTTGGCACGAAATAGGATATTTTGATCTCGCG
GCAATAACTGACTACGTTCTTAAAAAAACTACTGCACAAAAGCTTGATTTTATTGCATTT
TCACAAGGCACGACGAGCCTGTTAGTTTTGTTATCGTCTCGTCCAGAATATAATTCTAAA
ATTAGACAAGCACATTTAATGGCACCGCCTGCTTTTAGAAAGAAGTTACCCAAGTCGCAA
GTTGTCTTTAGCGTCTTAAAATTCTTGGACAGGCATAATGATGAAATCAGGTTTTGGGAT
TTGAAACGTTTGTTTCGCATAGGAAAAAATATTAGCAAAACAATATGCAGAGACAATGAC
CTCTTGTCGTTTCGTTTATGCAAATTCTTGATTCTGAGCGTTTTTAGTACTGATAATAGA
AGAGAACTTGAAATTGAAACTAAAGTACTTCCACATCTTATTAATTACATGTCACCCCGA
GTTTCAGTCATGCAGTTGACCCACTATTATCAAAATATGATTGCTAATAAATTTCGACAA
TTCGATTACAAGGATAAAAACTTTCAACATTACAATTCAACAACCCCACCAGATTATAAC
TTGTCAAAAATAACTGCACCTGTTTATTTATATCATGCTGGAAATGACCGATTTATTTCT
GAAGAGGGAGTAGCATACTTAAGAAGTCTTCTTCCAAATGTACAAGAATATCGAGTCATA
AGCAATTGGAGTCACATTGATTTTGTATATTCAAAATATTCACGAGACGTTCTATACAAC
AATATTCTTCATGCCTTGCTAGCAGTGAGTTATTAA
>g4538.t1 Gene=g4538 Length=391
MKLNSRFVVLILYYCVTLTLQDNPEGDQVLQLISSAGFQGEAHYTETDDGYELKIHRIVP
KIHNGREPVILMHGLLATAADFLITGPDIAIAYLLSNNGYDVYLGNSRGNKYSTKHRIYT
TDSTEYWRYSWHEIGYFDLAAITDYVLKKTTAQKLDFIAFSQGTTSLLVLLSSRPEYNSK
IRQAHLMAPPAFRKKLPKSQVVFSVLKFLDRHNDEIRFWDLKRLFRIGKNISKTICRDND
LLSFRLCKFLILSVFSTDNRRELEIETKVLPHLINYMSPRVSVMQLTHYYQNMIANKFRQ
FDYKDKNFQHYNSTTPPDYNLSKITAPVYLYHAGNDRFISEEGVAYLRSLLPNVQEYRVI
SNWSHIDFVYSKYSRDVLYNNILHALLAVSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4538.t1 | Gene3D | G3DSA:3.40.50.1820 | - | 20 | 387 | 1.6E-102 |
| 2 | g4538.t1 | PANTHER | PTHR11005:SF127 | LIPASE-RELATED | 9 | 386 | 3.3E-105 |
| 3 | g4538.t1 | PANTHER | PTHR11005 | LYSOSOMAL ACID LIPASE-RELATED | 9 | 386 | 3.3E-105 |
| 12 | g4538.t1 | PIRSF | PIRSF000862 | Steryl_ester_lip | 5 | 390 | 7.8E-89 |
| 1 | g4538.t1 | Pfam | PF00561 | alpha/beta hydrolase fold | 68 | 369 | 1.4E-17 |
| 8 | g4538.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 9 | g4538.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 10 | g4538.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 16 | - |
| 11 | g4538.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 7 | g4538.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 391 | - |
| 4 | g4538.t1 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 29 | 384 | 3.38E-49 |
| 5 | g4538.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
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 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