General information for g5144.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Very long-chain-fatty-acid–CoA ligase bubblegum.
Parent gene
- The parent gene g5144 is located on chr_2: 7276993..7279664 (- 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 | g5144 | g5144.t1 | TTS | g5144.t1 | 7274932 | 7274932 |
| chr_2 | g5144 | g5144.t1 | isoform | g5144.t1 | 7275198 | 7277519 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon1 | 7275198 | 7275348 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS1 | 7275198 | 7275348 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon2 | 7275405 | 7275693 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS2 | 7275405 | 7275693 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon3 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS3 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon4 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS4 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon5 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS5 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon6 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS6 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t1 | exon | g5144.t1.exon7 | 7277185 | 7277519 |
| chr_2 | g5144 | g5144.t1 | cds | g5144.t1.CDS7 | 7277185 | 7277519 |
| chr_2 | g5144 | g5144.t1 | TSS | g5144.t1 | 7277915 | 7277915 |
Sequences
>g5144.t1 Gene=g5144 Length=1962
ATGGCTGGAACTGAAGATTTTCGTATAATTGATCCAACGAAGCGATTAAAACTTCGCATA
AATCCTGATAACAAGATTGCAAGCATCGATCCAATTTCAGTTCCTCAGTTACTATCAAAA
ATTGCAGAGAGTTTTCCTAATCATCCAGCTTTAAAGCAACGAAATGCAATCACCAAAGAT
TGGGAAACAGTCACTTACAGTGATTATAAGCAACGAGTTGAGAAAATGGCAAAAGTTTTT
ATTAAGTTAGGTTTAGAACGTTATGGAACAGTTGCTGTTCTTGCATTTAATAGCATCGAA
TGGTTTGTGTCAGAACTTGCAGCTATTCAAGCAGGTGGAATTGCAACTGGAATTTATACA
ACAAATTCAGTTCATTCAACACATCACGTTCTTGAGACATCTCGTGCTAATATTGTTATA
GTAGATGAAGCTAAACAAATGGAAAAGATTCGTGAAATTAAAGATAAGCTTCCAAATTTG
AAGGCAATTGTGCAGACATTACCGCCTTATGCACAGTACATTAAAAAAGAAGATGGTTTT
TGGCGTTGGAATGAAATTGAAGAGCTCAATACTGCTGATGTTGATGAAGAATATCAACAG
AGACTTAAAAGCATTACACCAGATGAATGTTGTTGTCTAGTTTATACATCTGGAACAACT
GGTAATCCCAAAGGAGCAATGTTGTGTCATGATAATTTTACGTGGATAACAAATAGTGTG
ACTGAATATTTGCCGAATTTGGAAATGGGGAAGGAAATCCTCGTATCATATCTTCCACTC
TCACACGTTGCTGCACAAACTTTAGATATTTATGTTACATTAGCATTAGCTGCAACTGTA
TATTTTGCTGATCGTGATGCATTGAAAGGAACACTATTAAAAACTCTCACTGAAGCGCGA
CCAACTGTTTTCTTGGGTGTGCCGAGAGTGTATGAAAAAATTCAGGAAAAGATGATGCAA
GCTGGCTCACAATCAGGCGCTTTGAAACGTACACTTGGTTCATGGGCTAAAAGCGTCACT
CTTCAATATCATTTGGATTGCATGGCTGGTAATTATTATACTGGATTCCAATATAAACTT
GCAACAAAGTTGTTACTTAGCAAAGTCAAACATGCACTTGGCTTTGACCGAATCAAATTC
ATGATAACTGGTGCAGCACCGATGAGTGTCGAAACGAAAAAATACTTTCTGAGTCTTGAT
ATGCCTATTATTGAAGCATACGGAATGTCCGAATCAAGCGGTGCCCACTCAGTTGCTAAA
GTGCATGATCCATCTTTTGAATCTATTGGAAAAACACTACCAGGTATCGAGACAAAAATC
GATAATCCAAATGAGGAAGGTCATGGTGAAATTTGCAAACGTGGTAGAAATGTTTTTATG
GGATATATTGGGGAACTTGATAAAACTTTAGAGGCATTAGATGATGATGGATGGTTACAT
ACAGGCGATATCGGATATGTAGATGAAAATGGCTACCTTTTCATTACTGGCCGAATTAAA
GAGCTTGTTATTACTGCAGGAGGTGAAAATATTCCACCGGTACATATTGAGAATTTAGTC
AAGGCGGAATGCTCAGCAATTTCAAATGCATTTCTCGTTGGTGATAATCGTAAATTCCTT
ACAATTTTGATTTCTCTTAAGACTGAAGTCGATAAAGAAGGTGCTCCATTGGATGAACTT
GCACCTGAATCTCTTAAATTAATGAAATCGCTTAATTTAAATTATACAAAATTGAGTGAA
GTTCTCAATGCAGGTCCTGATGTGAAGGTTTCACAAGCCATACAAGACGCAATTGTTCGT
GCCAACAAAAGTTCCATTTCCAACGCTCAAAAAGTTCAAAAGTTTGCATTTTTACCACAT
GATTTTAGCATTCCTACAGGAGAGTTAGGACCAACACTTAAAATAAAAAGAAGCTACATC
TCAGAAAAGTACAAAGAGATCATCAATAAACTTTATCATTAG
>g5144.t1 Gene=g5144 Length=653
MAGTEDFRIIDPTKRLKLRINPDNKIASIDPISVPQLLSKIAESFPNHPALKQRNAITKD
WETVTYSDYKQRVEKMAKVFIKLGLERYGTVAVLAFNSIEWFVSELAAIQAGGIATGIYT
TNSVHSTHHVLETSRANIVIVDEAKQMEKIREIKDKLPNLKAIVQTLPPYAQYIKKEDGF
WRWNEIEELNTADVDEEYQQRLKSITPDECCCLVYTSGTTGNPKGAMLCHDNFTWITNSV
TEYLPNLEMGKEILVSYLPLSHVAAQTLDIYVTLALAATVYFADRDALKGTLLKTLTEAR
PTVFLGVPRVYEKIQEKMMQAGSQSGALKRTLGSWAKSVTLQYHLDCMAGNYYTGFQYKL
ATKLLLSKVKHALGFDRIKFMITGAAPMSVETKKYFLSLDMPIIEAYGMSESSGAHSVAK
VHDPSFESIGKTLPGIETKIDNPNEEGHGEICKRGRNVFMGYIGELDKTLEALDDDGWLH
TGDIGYVDENGYLFITGRIKELVITAGGENIPPVHIENLVKAECSAISNAFLVGDNRKFL
TILISLKTEVDKEGAPLDELAPESLKLMKSLNLNYTKLSEVLNAGPDVKVSQAIQDAIVR
ANKSSISNAQKVQKFAFLPHDFSIPTGELGPTLKIKRSYISEKYKEIINKLYH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5144.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 32 | 342 | 3.0E-52 |
| 7 | g5144.t1 | Gene3D | G3DSA:3.40.50.12780 | - | 359 | 498 | 7.2E-37 |
| 2 | g5144.t1 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 6 | 652 | 3.2E-238 |
| 3 | g5144.t1 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 6 | 652 | 3.2E-238 |
| 1 | g5144.t1 | Pfam | PF00501 | AMP-binding enzyme | 41 | 505 | 3.9E-94 |
| 5 | g5144.t1 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 213 | 224 | - |
| 4 | g5144.t1 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 30 | 652 | 5.1E-107 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5144/g5144.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K15013 (long-chain-fatty-acid–CoA ligase ACSBG)
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.
