General information for g12439.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Long-chain fatty acid transport protein 4.
Parent gene
- The parent gene g12439 is located on chr_1: 23620018..23623420 (+ 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 | g12439 | g12439.t1 | isoform | g12439.t1 | 23620018 | 23623420 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon1 | 23620018 | 23620229 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS1 | 23620018 | 23620229 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon2 | 23621344 | 23621494 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS2 | 23621344 | 23621494 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon3 | 23621559 | 23622000 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS3 | 23621559 | 23622000 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon4 | 23622063 | 23622185 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS4 | 23622063 | 23622185 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon5 | 23622247 | 23622901 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS5 | 23622247 | 23622901 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon6 | 23622962 | 23623052 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS6 | 23622962 | 23623052 |
| chr_1 | g12439 | g12439.t1 | exon | g12439.t1.exon7 | 23623112 | 23623420 |
| chr_1 | g12439 | g12439.t1 | cds | g12439.t1.CDS7 | 23623112 | 23623420 |
| chr_1 | g12439 | g12439.t1 | TTS | g12439.t1 | 23623605 | 23623605 |
| chr_1 | g12439 | g12439.t1 | TSS | g12439.t1 | NA | NA |
Sequences
>g12439.t1 Gene=g12439 Length=1983
ATGACTGAACTAAAATTAAAAACAAAATTAACAATTAATGAAAAAATTGCAACACTTACC
GGAATCGTTGCTTTTGGAACATTTCTATCATCAGCAATTGGAAAGCATCTTTTTCCGCAA
GCACTTCTCTCCGTACTGATATGGTTCCTCATCACGGGTCGACGTCCTTCTATCATTTTC
GCCTTTGTCATTAAAATTCGACGTGATTTAATTGCGGCAAAACGGTATTTGCTAATGCTT
GCAATGTTAAAGAAATGGGAAAATAATAATGACTCTGTTGCAAGTGTATTTCGTAAAAAT
GTCAAAAATAAACAAAATAAACCAGCATTCATAATGGATGATAAGAAAATCACTTTCCAG
GAGATGGAAAATCTTAGTAATAAAATTGGAAGATACTTTAAGCAAAAAGGATTTAAGAAA
GGTGACACCATATCATTAGTAATGGAAACAAGATTAGAATATGCATCAATGTGGCTTGGC
TTATCGAAAATCGGTGTCATAACGGCATTGATCAATTATAATTTACGCAAAGAAACGCTC
ATTCATTCCATCCGTGTCGCATCATCGAAAGCAATCATTGTAAGCACAGAGTTGCTTGAT
GCCATTAAAGAAATACTTCATGATGAAGAAATTAGTAAAATGAAAATTTATGTCTATGAC
AATCAAAATGAAAAGGTTGAACTGATTAATAGTAATAGTGTAAATTTACATCGCGAACTG
GAAAATATTTCATCAGATACATTTGATATAAGCGATATCTTGCCAAAAGATAGACTTTTT
TATATATACACAAGTGGAACAACTGGAATGCCTAAAGCAGCAGTCATAACAAATTTACGC
TTCATGTTTATGGTGTCTGGTGTTTTCAGAATGTTTGGAATGAGTGACAGTGACATTATT
TATAACACTCTTCCACTTTATCATACAGCTGGCGGTATGTTAGGTGTTGGATCTGTTGTT
CTCTTTACTGTAACAATGGCATTGCGAAAGAAATTTTCAGCATCAAATTTTTGGACTGAT
TGCATCAAATATAATTGTAATGTTGCGCAATATATTGGAGAACTTTGTAGATTTTTACTA
ATGACACCTGAAAAACCAGAAGATAAAAAGCACAATGTCAGACTAATGTTTGGTAATGGT
CTTCGTCCACAAATTTGGCCTGATTTTGTGAAACGTTTCAACATCAAACAAATTGGAGAA
GCTTATGGTGCAACTGAATCAAATACAAATCTTGCAAATTGCGACAATCAGGTCGGAGCA
GTCGGCTTTGTGCCACAAGTTGCAACTCATCTTTATCCGGTAGATTTAATTAAATGCGAT
GAAGAAACAGGCGAACCGATAAGGAATGAAAACGGTTTTTGTATTCGTTGTAATTATGGT
GAGGCAGGAGTTTTTGTTGGGAAAATTAATCAAAATCATGCAGCAAGATCATTTGCCGGA
TATGCTGATAAGAAGGCATCAGAAAAGAAAGTTTTAAAAGATGTTTTCAAAAAAGGCGAT
ATGTATTTCAATTCATCTGATATACTCGTAATGGACATTTATGGTTATTACTATTTTAAA
GATCGAACTGGTGATACATACAGATGGAGAGGTGAAAATGTAGCAACATCAGAAGTCGAA
GGAATTATCATGCGTGTCGCTGGCTTGACTGATTGCGTAGTTTATGGTGTTGATATACCA
AATACAGAAGGAAAGGCAGGAATGGCAGCTATTGTTGATCCTCACAATCAATTAGATATG
GAAAAACTTGCAGCAGGAATTAGGGAACATCTTCCAATATATGCTAGACCAGTTTTCATT
AGAATTTTACCGCAGCTACCAATGACTGGAACGTTTAAACTTAAAAAAAGAGATTTGCAA
CTTGAAGGTTTTGATATTACAAAAATTAGTGATTCAATCTATTTATTACAATCTGATGGA
TCATATAAGAAAATGTCATTTGATCAATATAATTCAATTAAAGAGGGACGCGCTAAGCTG
TGA
>g12439.t1 Gene=g12439 Length=660
MTELKLKTKLTINEKIATLTGIVAFGTFLSSAIGKHLFPQALLSVLIWFLITGRRPSIIF
AFVIKIRRDLIAAKRYLLMLAMLKKWENNNDSVASVFRKNVKNKQNKPAFIMDDKKITFQ
EMENLSNKIGRYFKQKGFKKGDTISLVMETRLEYASMWLGLSKIGVITALINYNLRKETL
IHSIRVASSKAIIVSTELLDAIKEILHDEEISKMKIYVYDNQNEKVELINSNSVNLHREL
ENISSDTFDISDILPKDRLFYIYTSGTTGMPKAAVITNLRFMFMVSGVFRMFGMSDSDII
YNTLPLYHTAGGMLGVGSVVLFTVTMALRKKFSASNFWTDCIKYNCNVAQYIGELCRFLL
MTPEKPEDKKHNVRLMFGNGLRPQIWPDFVKRFNIKQIGEAYGATESNTNLANCDNQVGA
VGFVPQVATHLYPVDLIKCDEETGEPIRNENGFCIRCNYGEAGVFVGKINQNHAARSFAG
YADKKASEKKVLKDVFKKGDMYFNSSDILVMDIYGYYYFKDRTGDTYRWRGENVATSEVE
GIIMRVAGLTDCVVYGVDIPNTEGKAGMAAIVDPHNQLDMEKLAAGIREHLPIYARPVFI
RILPQLPMTGTFKLKKRDLQLEGFDITKISDSIYLLQSDGSYKKMSFDQYNSIKEGRAKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12439.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 82 | 525 | 9.3E-64 |
| 11 | g12439.t1 | Gene3D | G3DSA:3.30.300.30 | - | 526 | 623 | 4.7E-14 |
| 3 | g12439.t1 | PANTHER | PTHR43107:SF21 | FATTY ACID (LONG CHAIN) TRANSPORT PROTEIN, ISOFORM F-RELATED | 11 | 658 | 2.0E-240 |
| 4 | g12439.t1 | PANTHER | PTHR43107 | LONG-CHAIN FATTY ACID TRANSPORT PROTEIN | 11 | 658 | 2.0E-240 |
| 2 | g12439.t1 | Pfam | PF00501 | AMP-binding enzyme | 97 | 529 | 6.0E-62 |
| 1 | g12439.t1 | Pfam | PF13193 | AMP-binding enzyme C-terminal domain | 538 | 613 | 9.9E-10 |
| 12 | g12439.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 18 | g12439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 33 | - |
| 15 | g12439.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 34 | 44 | - |
| 17 | g12439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 13 | g12439.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 65 | 272 | - |
| 19 | g12439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 273 | 293 | - |
| 16 | g12439.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 294 | 304 | - |
| 20 | g12439.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 305 | 328 | - |
| 14 | g12439.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 329 | 660 | - |
| 9 | g12439.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 261 | 272 | - |
| 8 | g12439.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 91 | 621 | 6.28E-93 |
| 7 | g12439.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 34 | - |
| 6 | g12439.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 44 | 66 | - |
| 5 | g12439.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 304 | 326 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K08745 (solute carrier family 27 (fatty acid transporter), member 1/4 [EC:6.2.1.-])
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.
