Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Lipase 3.

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_1 g12349 g12349.t2 TSS g12349.t2 22722897 22722897
chr_1 g12349 g12349.t2 isoform g12349.t2 22722938 22724299
chr_1 g12349 g12349.t2 exon g12349.t2.exon1 22722938 22723024
chr_1 g12349 g12349.t2 cds g12349.t2.CDS1 22722938 22723024
chr_1 g12349 g12349.t2 exon g12349.t2.exon2 22723083 22723566
chr_1 g12349 g12349.t2 cds g12349.t2.CDS2 22723083 22723493
chr_1 g12349 g12349.t2 exon g12349.t2.exon3 22723847 22723913
chr_1 g12349 g12349.t2 exon g12349.t2.exon4 22723969 22724299
chr_1 g12349 g12349.t2 TTS g12349.t2 22724340 22724340

Sequences

>g12349.t2 Gene=g12349 Length=969
ATGAAAACTGCACAAATTTTAATTGTTTTTTTGGCATTATTTTCTGTTGTGTTTGCTGAT
GTTTGGGAAGATACACAATTAAATACAATTCAACTTTTAAGAAAGTATGGCTATACAGCA
GAAGAATATTCAGTAACAACATCAGATGGTTATCGATTAGGTATTCATCGTTGTTCTGGT
GGTCCAGTTTCACCACCAGCTGCTAATAAGCCAGTAGCATTTCTTATGCATGGACAACTT
AGTTCATCTGCTGATTATGTAATTATGGGTCCACAAGTTTCACTAGCTTATATGCTATCT
GATCTTGGTTATGATGTATGGATGGGAAATTCACATGGAAATAGATATTCAAATACTCAT
ACATCACTTAATAATGAAACAAAAGCTTATTGGGATTTTTCATGGCATGAAATAGGTTCA
ATTGATGTTCCTACAATGATTGACTATATTTTAGCGAGAACAGGACAAAGAAATTTGCAT
TATATTGGTAAGTCATAATAATTATGTATAAAAATAGTTGTTAATTCATAAATTTATTAA
AGGTCATTCAATGGGAACAACAGTTTATTTTAAACAAATCGAACAATGTTGCCAGTTATG
AATGCACATTCACCTGCTGGAGCAAGCATGATGAATATGTTGCATTATGCTCAAATAGTA
AGAAGTGGAATTTTCCAACAATATGATCATGGTGTCAATAATATCTACAGATATGGTCAA
TTAACACCTCCATTATATAGATTCACTGGTCATACTGCACCATTACATTTATTTTGGTCA
ACAAATGATTGGATGGCAACACCAGCTGATGTATCGACACTTTATAATCGATTAGGTGGT
TCAAGTGTTGTAGATTTATTTTATCATGTACCACAAGTTGAATGGAATCATATGGACTTT
GTTTGGGGTATTAATGTTAGACGTTTGGTTTATAACAGAATGGTTGAAGAAATGAGAAAA
TATGACTGA

>g12349.t2 Gene=g12349 Length=165
MKTAQILIVFLALFSVVFADVWEDTQLNTIQLLRKYGYTAEEYSVTTSDGYRLGIHRCSG
GPVSPPAANKPVAFLMHGQLSSSADYVIMGPQVSLAYMLSDLGYDVWMGNSHGNRYSNTH
TSLNNETKAYWDFSWHEIGSIDVPTMIDYILARTGQRNLHYIGKS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12349.t2 Gene3D G3DSA:3.40.50.1820 - 18 165 2.4E-56
2 g12349.t2 PANTHER PTHR11005:SF127 LIPASE-RELATED 5 165 7.9E-58
3 g12349.t2 PANTHER PTHR11005 LYSOSOMAL ACID LIPASE-RELATED 5 165 7.9E-58
1 g12349.t2 Pfam PF04083 Partial alpha/beta-hydrolase lipase region 31 89 4.6E-18
8 g12349.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
9 g12349.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 2 -
10 g12349.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 3 14 -
11 g12349.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
7 g12349.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 165 -
4 g12349.t2 SUPERFAMILY SSF53474 alpha/beta-Hydrolases 24 165 1.39E-23
5 g12349.t2 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:0006629 lipid metabolic process BP

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