Gene loci information

Transcript annotation

  • This transcript has been annotated as 1-acyl-sn-glycerol-3-phosphate acyltransferase delta.

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_3 g2454 g2454.t3 TTS g2454.t3 18050260 18050260
chr_3 g2454 g2454.t3 isoform g2454.t3 18050508 18053464
chr_3 g2454 g2454.t3 exon g2454.t3.exon1 18050508 18050584
chr_3 g2454 g2454.t3 cds g2454.t3.CDS1 18050508 18050584
chr_3 g2454 g2454.t3 exon g2454.t3.exon2 18050659 18051543
chr_3 g2454 g2454.t3 cds g2454.t3.CDS2 18050659 18051543
chr_3 g2454 g2454.t3 exon g2454.t3.exon3 18053162 18053354
chr_3 g2454 g2454.t3 cds g2454.t3.CDS3 18053162 18053339
chr_3 g2454 g2454.t3 exon g2454.t3.exon4 18053433 18053464
chr_3 g2454 g2454.t3 TSS g2454.t3 18053481 18053481

Sequences

>g2454.t3 Gene=g2454 Length=1187
CGTTGCACGATAATGTACAAGTTGTAATTTTCTTAATTTAAGCAAAAATGGCAAGCGGGT
TTTTGAAGCAAAATATTATATCGCATCTACTGATAACAGCGACAATCTTAACATCGGGAA
TTATAGTGAATATTATTCAGGTGCTATTGCACATACTCGTTAAGCCTTTCAATAAACGGC
TCTTTCATCATTGCATGTATTATGTTTCATGGACATGGCTAGCACAGTGCGTATTTGTCA
TTGATTTCTGGTCAAGTTCTGAACTTATAGTATATTGCAATGAAGAAGATTTGAAGTACA
TTGGAAATGAGCATAATTTCACACTCATCAATCATTCATATGAAATTGATTGGCTTGTTG
GATGGTTATTAATTGAAAAATTCCGTGGTTTAGGATGTACTCGTGGTTTCATTAAAAATG
CTATCAAATACATTCCTATATGCGGATGGTTTTTTGGCTTTGCCGAGCATGTTTTTTTAC
AGAGATCATTCGATAAAGATAAGAAAGTCATTGAAAATAGAATTTCTGAATACATGACCT
ATCCAAATTCTACTTGGATTGTGGTCACAGCTGAAGGCACAAGATTCACAAAAGAAAAAC
ATGAAACGTCAATTAAATTTGCAAAAGAAAAGAATGTTGAACCACTTAAGCATCATCTCA
TACCTAGAGCACGCGGATTTGCTACATGCATTCCATTATTGAAAAAGTACAATTGTCCAG
TAATTTATAATGTTCAACTTGCCTTTGAAAAAGATGCAAAAGTTGCACCAACATTGGGTA
ATTTGTTATTAGGCAAAAAAGTCGTCGCACATCTTTTTATTGAGCGAATTCCAATGGAGA
AAGCAGAACCGACTTTTGAATTCTTATACGATGTTTATAAAGAAAAGGATGCGCTCCAAG
ATAGTTTTCATAAATTTGGAAACTTTTATGAAGGTCGAGGACTAAAACCAGTTGAGGGTG
TGAGAATGAAACCAAGACTACGCATACTTATTAATACAGTAATTTGGATAATTTTTTCAA
TATTCCTAATGACTTATTACACAATCAAATTGATTCTTGCTGAACGATATTTTTTGCTCA
CGACAGTTAGCGTTGGCATTATTGCAATGCTTTATTTTATGCTCCAAAATATCCTACGTC
ATTCGAAAGTCAATAAGTCAGGATCACAATATGGAAAATCACGATGA

>g2454.t3 Gene=g2454 Length=379
MASGFLKQNIISHLLITATILTSGIIVNIIQVLLHILVKPFNKRLFHHCMYYVSWTWLAQ
CVFVIDFWSSSELIVYCNEEDLKYIGNEHNFTLINHSYEIDWLVGWLLIEKFRGLGCTRG
FIKNAIKYIPICGWFFGFAEHVFLQRSFDKDKKVIENRISEYMTYPNSTWIVVTAEGTRF
TKEKHETSIKFAKEKNVEPLKHHLIPRARGFATCIPLLKKYNCPVIYNVQLAFEKDAKVA
PTLGNLLLGKKVVAHLFIERIPMEKAEPTFEFLYDVYKEKDALQDSFHKFGNFYEGRGLK
PVEGVRMKPRLRILINTVIWIIFSIFLMTYYTIKLILAERYFLLTTVSVGIIAMLYFMLQ
NILRHSKVNKSGSQYGKSR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g2454.t3 CDD cd07990 LPLAT_LCLAT1-like 62 259 5.35038E-51
3 g2454.t3 PANTHER PTHR10983:SF24 MIP21173P-RELATED 10 333 2.8E-70
4 g2454.t3 PANTHER PTHR10983 1-ACYLGLYCEROL-3-PHOSPHATE ACYLTRANSFERASE-RELATED 10 333 2.8E-70
2 g2454.t3 Pfam PF01553 Acyltransferase 91 195 6.1E-12
1 g2454.t3 Pfam PF16076 Acyltransferase C-terminus 245 320 1.5E-12
13 g2454.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
16 g2454.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 37 -
12 g2454.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 38 48 -
19 g2454.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 68 -
15 g2454.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 69 124 -
20 g2454.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 125 144 -
10 g2454.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 145 312 -
18 g2454.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 313 333 -
14 g2454.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 334 338 -
17 g2454.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 339 359 -
11 g2454.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 360 379 -
9 g2454.t3 SMART SM00563 plsc_2 90 212 9.4E-8
8 g2454.t3 SUPERFAMILY SSF69593 Glycerol-3-phosphate (1)-acyltransferase 12 195 4.18E-6
6 g2454.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
7 g2454.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 314 336 -
5 g2454.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 341 363 -

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:0016746 acyltransferase activity 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.

Raw TPM values