General information for g2454.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 1-acyl-sn-glycerol-3-phosphate acyltransferase delta.
Parent gene
- The parent gene g2454 is located on chr_3: 18050508..18053464 (- 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_3 | g2454 | g2454.t1 | TTS | g2454.t1 | 18050260 | 18050260 |
| chr_3 | g2454 | g2454.t1 | isoform | g2454.t1 | 18050508 | 18053339 |
| chr_3 | g2454 | g2454.t1 | exon | g2454.t1.exon1 | 18050508 | 18050584 |
| chr_3 | g2454 | g2454.t1 | cds | g2454.t1.CDS1 | 18050508 | 18050584 |
| chr_3 | g2454 | g2454.t1 | exon | g2454.t1.exon2 | 18050659 | 18051543 |
| chr_3 | g2454 | g2454.t1 | cds | g2454.t1.CDS2 | 18050659 | 18051543 |
| chr_3 | g2454 | g2454.t1 | exon | g2454.t1.exon3 | 18053162 | 18053339 |
| chr_3 | g2454 | g2454.t1 | cds | g2454.t1.CDS3 | 18053162 | 18053339 |
| chr_3 | g2454 | g2454.t1 | TSS | g2454.t1 | 18053481 | 18053481 |
Sequences
>g2454.t1 Gene=g2454 Length=1140
ATGGCAAGCGGGTTTTTGAAGCAAAATATTATATCGCATCTACTGATAACAGCGACAATC
TTAACATCGGGAATTATAGTGAATATTATTCAGGTGCTATTGCACATACTCGTTAAGCCT
TTCAATAAACGGCTCTTTCATCATTGCATGTATTATGTTTCATGGACATGGCTAGCACAG
TGCGTATTTGTCATTGATTTCTGGTCAAGTTCTGAACTTATAGTATATTGCAATGAAGAA
GATTTGAAGTACATTGGAAATGAGCATAATTTCACACTCATCAATCATTCATATGAAATT
GATTGGCTTGTTGGATGGTTATTAATTGAAAAATTCCGTGGTTTAGGATGTACTCGTGGT
TTCATTAAAAATGCTATCAAATACATTCCTATATGCGGATGGTTTTTTGGCTTTGCCGAG
CATGTTTTTTTACAGAGATCATTCGATAAAGATAAGAAAGTCATTGAAAATAGAATTTCT
GAATACATGACCTATCCAAATTCTACTTGGATTGTGGTCACAGCTGAAGGCACAAGATTC
ACAAAAGAAAAACATGAAACGTCAATTAAATTTGCAAAAGAAAAGAATGTTGAACCACTT
AAGCATCATCTCATACCTAGAGCACGCGGATTTGCTACATGCATTCCATTATTGAAAAAG
TACAATTGTCCAGTAATTTATAATGTTCAACTTGCCTTTGAAAAAGATGCAAAAGTTGCA
CCAACATTGGGTAATTTGTTATTAGGCAAAAAAGTCGTCGCACATCTTTTTATTGAGCGA
ATTCCAATGGAGAAAGCAGAACCGACTTTTGAATTCTTATACGATGTTTATAAAGAAAAG
GATGCGCTCCAAGATAGTTTTCATAAATTTGGAAACTTTTATGAAGGTCGAGGACTAAAA
CCAGTTGAGGGTGTGAGAATGAAACCAAGACTACGCATACTTATTAATACAGTAATTTGG
ATAATTTTTTCAATATTCCTAATGACTTATTACACAATCAAATTGATTCTTGCTGAACGA
TATTTTTTGCTCACGACAGTTAGCGTTGGCATTATTGCAATGCTTTATTTTATGCTCCAA
AATATCCTACGTCATTCGAAAGTCAATAAGTCAGGATCACAATATGGAAAATCACGATGA
>g2454.t1 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.t1 | CDD | cd07990 | LPLAT_LCLAT1-like | 62 | 259 | 5.35038E-51 |
| 3 | g2454.t1 | PANTHER | PTHR10983:SF24 | MIP21173P-RELATED | 10 | 333 | 2.8E-70 |
| 4 | g2454.t1 | PANTHER | PTHR10983 | 1-ACYLGLYCEROL-3-PHOSPHATE ACYLTRANSFERASE-RELATED | 10 | 333 | 2.8E-70 |
| 2 | g2454.t1 | Pfam | PF01553 | Acyltransferase | 91 | 195 | 6.1E-12 |
| 1 | g2454.t1 | Pfam | PF16076 | Acyltransferase C-terminus | 245 | 320 | 1.5E-12 |
| 13 | g2454.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 11 | - |
| 16 | g2454.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 37 | - |
| 12 | g2454.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 38 | 48 | - |
| 19 | g2454.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 49 | 68 | - |
| 15 | g2454.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 69 | 124 | - |
| 20 | g2454.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 125 | 144 | - |
| 10 | g2454.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 145 | 312 | - |
| 18 | g2454.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 313 | 333 | - |
| 14 | g2454.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 334 | 338 | - |
| 17 | g2454.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 339 | 359 | - |
| 11 | g2454.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 360 | 379 | - |
| 9 | g2454.t1 | SMART | SM00563 | plsc_2 | 90 | 212 | 9.4E-8 |
| 8 | g2454.t1 | SUPERFAMILY | SSF69593 | Glycerol-3-phosphate (1)-acyltransferase | 12 | 195 | 4.18E-6 |
| 6 | g2454.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 15 | 37 | - |
| 7 | g2454.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 314 | 336 | - |
| 5 | g2454.t1 | 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.
