General information for g5144.t7
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.t7 | TTS | g5144.t7 | 7274932 | 7274932 |
| chr_2 | g5144 | g5144.t7 | isoform | g5144.t7 | 7275879 | 7277526 |
| chr_2 | g5144 | g5144.t7 | exon | g5144.t7.exon1 | 7275879 | 7275980 |
| chr_2 | g5144 | g5144.t7 | cds | g5144.t7.CDS1 | 7275880 | 7275980 |
| chr_2 | g5144 | g5144.t7 | exon | g5144.t7.exon2 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t7 | cds | g5144.t7.CDS2 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t7 | exon | g5144.t7.exon3 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t7 | cds | g5144.t7.CDS3 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t7 | exon | g5144.t7.exon4 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t7 | cds | g5144.t7.CDS4 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t7 | exon | g5144.t7.exon5 | 7277185 | 7277526 |
| chr_2 | g5144 | g5144.t7 | cds | g5144.t7.CDS5 | 7277185 | 7277519 |
| chr_2 | g5144 | g5144.t7 | TSS | g5144.t7 | 7277915 | 7277915 |
Sequences
>g5144.t7 Gene=g5144 Length=1412
AGATTAAATGGCTGGAACTGAAGATTTTCGTATAATTGATCCAACGAAGCGATTAAAACT
TCGCATAAATCCTGATAACAAGATTGCAAGCATCGATCCAATTTCAGTTCCTCAGTTACT
ATCAAAAATTGCAGAGAGTTTTCCTAATCATCCAGCTTTAAAGCAACGAAATGCAATCAC
CAAAGATTGGGAAACAGTCACTTACAGTGATTATAAGCAACGAGTTGAGAAAATGGCAAA
AGTTTTTATTAAGTTAGGTTTAGAACGTTATGGAACAGTTGCTGTTCTTGCATTTAATAG
CATCGAATGGTTTGTGTCAGAACTTGCAGCTATTCAAGCAGGTGGAATTGCAACTGGAAT
TTATACAACAAATTCAGTTCATTCAACACATCACGTTCTTGAGACATCTCGTGCTAATAT
TGTTATAGTAGATGAAGCTAAACAAATGGAAAAGATTCGTGAAATTAAAGATAAGCTTCC
AAATTTGAAGGCAATTGTGCAGACATTACCGCCTTATGCACAGTACATTAAAAAAGAAGA
TGGTTTTTGGCGTTGGAATGAAATTGAAGAGCTCAATACTGCTGATGTTGATGAAGAATA
TCAACAGAGACTTAAAAGCATTACACCAGATGAATGTTGTTGTCTAGTTTATACATCTGG
AACAACTGGTAATCCCAAAGGAGCAATGTTGTGTCATGATAATTTTACGTGGATAACAAA
TAGTGTGACTGAATATTTGCCGAATTTGGAAATGGGGAAGGAAATCCTCGTATCATATCT
TCCACTCTCACACGTTGCTGCACAAACTTTAGATATTTATGTTACATTAGCATTAGCTGC
AACTGTATATTTTGCTGATCGTGATGCATTGAAAGGAACACTATTAAAAACTCTCACTGA
AGCGCGACCAACTGTTTTCTTGGGTGTGCCGAGAGTGTATGAAAAAATTCAGGAAAAGAT
GATGCAAGCTGGCTCACAATCAGGCGCTTTGAAACGTACACTTGGTTCATGGGCTAAAAG
CGTCACTCTTCAATATCATTTGGATTGCATGGCTGGTAATTATTATACTGGATTCCAATA
TAAACTTGCAACAAAGTTGTTACTTAGCAAAGTCAAACATGCACTTGGCTTTGACCGAAT
CAAATTCATGATAACTGGTGCAGCACCGATGAGTGTCGAAACGAAAAAATACTTTCTGAG
TCTTGATATGCCTATTATTGAAGCATACGGAATGTCCGAATCAAGCGGTGCCCACTCAGT
TGCTAAAGTGCATGATCCATCTTTTGAATCTATTGGAAAAACACTACCAGGTATCGAGAC
AAAAATCGATAATCCAAATGAGGAAGGTCATGGTGAAATTTGCAAACGTGGTAGAAATGT
TTTTATGGGATATATTGGGGAACTTGATAAAA
>g5144.t7 Gene=g5144 Length=468
MAGTEDFRIIDPTKRLKLRINPDNKIASIDPISVPQLLSKIAESFPNHPALKQRNAITKD
WETVTYSDYKQRVEKMAKVFIKLGLERYGTVAVLAFNSIEWFVSELAAIQAGGIATGIYT
TNSVHSTHHVLETSRANIVIVDEAKQMEKIREIKDKLPNLKAIVQTLPPYAQYIKKEDGF
WRWNEIEELNTADVDEEYQQRLKSITPDECCCLVYTSGTTGNPKGAMLCHDNFTWITNSV
TEYLPNLEMGKEILVSYLPLSHVAAQTLDIYVTLALAATVYFADRDALKGTLLKTLTEAR
PTVFLGVPRVYEKIQEKMMQAGSQSGALKRTLGSWAKSVTLQYHLDCMAGNYYTGFQYKL
ATKLLLSKVKHALGFDRIKFMITGAAPMSVETKKYFLSLDMPIIEAYGMSESSGAHSVAK
VHDPSFESIGKTLPGIETKIDNPNEEGHGEICKRGRNVFMGYIGELDK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5144.t7 | Gene3D | G3DSA:3.40.50.12780 | - | 32 | 342 | 1.3E-52 |
| 7 | g5144.t7 | Gene3D | G3DSA:3.40.50.12780 | - | 359 | 468 | 1.6E-20 |
| 2 | g5144.t7 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 5 | 465 | 9.3E-160 |
| 3 | g5144.t7 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 5 | 465 | 9.3E-160 |
| 1 | g5144.t7 | Pfam | PF00501 | AMP-binding enzyme | 41 | 465 | 1.4E-76 |
| 5 | g5144.t7 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 213 | 224 | - |
| 4 | g5144.t7 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 30 | 464 | 7.46E-76 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5144/g5144.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t7.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
