General information for g5144.t6
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.t6 | isoform | g5144.t6 | 7275407 | 7279047 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon1 | 7275407 | 7275693 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS1 | 7275407 | 7275693 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon2 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS2 | 7275762 | 7275980 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon3 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS3 | 7276044 | 7276190 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon4 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS4 | 7276246 | 7276740 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon5 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS5 | 7276800 | 7277125 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon6 | 7277185 | 7277524 |
| chr_2 | g5144 | g5144.t6 | cds | g5144.t6.CDS6 | 7277185 | 7277519 |
| chr_2 | g5144 | g5144.t6 | TTS | g5144.t6 | 7278428 | 7278428 |
| chr_2 | g5144 | g5144.t6 | exon | g5144.t6.exon7 | 7278845 | 7279047 |
| chr_2 | g5144 | g5144.t6 | TSS | g5144.t6 | 7278991 | 7278991 |
Sequences
>g5144.t6 Gene=g5144 Length=2017
TTGACTAACGTCGATGTGGCGCGCTCAAAATTTTTTTTACTATACACTCATTTTCATTTG
ACGCTAGAATATCGCAGCGACAAGACATATTTGTCGAGTCGAGCATATTTAGTGTGTGCC
CGGCTTTACTTTGTGAGAAGTGAAATAATAATTATTTCTCTGAAATACATATTATATTTT
TTGTTATCATTCATAATTCAAGCATTAAATGGCTGGAACTGAAGATTTTCGTATAATTGA
TCCAACGAAGCGATTAAAACTTCGCATAAATCCTGATAACAAGATTGCAAGCATCGATCC
AATTTCAGTTCCTCAGTTACTATCAAAAATTGCAGAGAGTTTTCCTAATCATCCAGCTTT
AAAGCAACGAAATGCAATCACCAAAGATTGGGAAACAGTCACTTACAGTGATTATAAGCA
ACGAGTTGAGAAAATGGCAAAAGTTTTTATTAAGTTAGGTTTAGAACGTTATGGAACAGT
TGCTGTTCTTGCATTTAATAGCATCGAATGGTTTGTGTCAGAACTTGCAGCTATTCAAGC
AGGTGGAATTGCAACTGGAATTTATACAACAAATTCAGTTCATTCAACACATCACGTTCT
TGAGACATCTCGTGCTAATATTGTTATAGTAGATGAAGCTAAACAAATGGAAAAGATTCG
TGAAATTAAAGATAAGCTTCCAAATTTGAAGGCAATTGTGCAGACATTACCGCCTTATGC
ACAGTACATTAAAAAAGAAGATGGTTTTTGGCGTTGGAATGAAATTGAAGAGCTCAATAC
TGCTGATGTTGATGAAGAATATCAACAGAGACTTAAAAGCATTACACCAGATGAATGTTG
TTGTCTAGTTTATACATCTGGAACAACTGGTAATCCCAAAGGAGCAATGTTGTGTCATGA
TAATTTTACGTGGATAACAAATAGTGTGACTGAATATTTGCCGAATTTGGAAATGGGGAA
GGAAATCCTCGTATCATATCTTCCACTCTCACACGTTGCTGCACAAACTTTAGATATTTA
TGTTACATTAGCATTAGCTGCAACTGTATATTTTGCTGATCGTGATGCATTGAAAGGAAC
ACTATTAAAAACTCTCACTGAAGCGCGACCAACTGTTTTCTTGGGTGTGCCGAGAGTGTA
TGAAAAAATTCAGGAAAAGATGATGCAAGCTGGCTCACAATCAGGCGCTTTGAAACGTAC
ACTTGGTTCATGGGCTAAAAGCGTCACTCTTCAATATCATTTGGATTGCATGGCTGGTAA
TTATTATACTGGATTCCAATATAAACTTGCAACAAAGTTGTTACTTAGCAAAGTCAAACA
TGCACTTGGCTTTGACCGAATCAAATTCATGATAACTGGTGCAGCACCGATGAGTGTCGA
AACGAAAAAATACTTTCTGAGTCTTGATATGCCTATTATTGAAGCATACGGAATGTCCGA
ATCAAGCGGTGCCCACTCAGTTGCTAAAGTGCATGATCCATCTTTTGAATCTATTGGAAA
AACACTACCAGGTATCGAGACAAAAATCGATAATCCAAATGAGGAAGGTCATGGTGAAAT
TTGCAAACGTGGTAGAAATGTTTTTATGGGATATATTGGGGAACTTGATAAAACTTTAGA
GGCATTAGATGATGATGGATGGTTACATACAGGCGATATCGGATATGTAGATGAAAATGG
CTACCTTTTCATTACTGGCCGAATTAAAGAGCTTGTTATTACTGCAGGAGGTGAAAATAT
TCCACCGGTACATATTGAGAATTTAGTCAAGGCGGAATGCTCAGCAATTTCAAATGCATT
TCTCGTTGGTGATAATCGTAAATTCCTTACAATTTTGATTTCTCTTAAGACTGAAGTCGA
TAAAGAAGGTGCTCCATTGGATGAACTTGCACCTGAATCTCTTAAATTAATGAAATCGCT
TAATTTAAATTATACAAAATTGAGTGAAGTTCTCAATGCAGGTCCTGATGTGAAGGTTTC
ACAAGCCATACAAGACGCAATTGTTCGTGCCAACAAA
>g5144.t6 Gene=g5144 Length=603
MAGTEDFRIIDPTKRLKLRINPDNKIASIDPISVPQLLSKIAESFPNHPALKQRNAITKD
WETVTYSDYKQRVEKMAKVFIKLGLERYGTVAVLAFNSIEWFVSELAAIQAGGIATGIYT
TNSVHSTHHVLETSRANIVIVDEAKQMEKIREIKDKLPNLKAIVQTLPPYAQYIKKEDGF
WRWNEIEELNTADVDEEYQQRLKSITPDECCCLVYTSGTTGNPKGAMLCHDNFTWITNSV
TEYLPNLEMGKEILVSYLPLSHVAAQTLDIYVTLALAATVYFADRDALKGTLLKTLTEAR
PTVFLGVPRVYEKIQEKMMQAGSQSGALKRTLGSWAKSVTLQYHLDCMAGNYYTGFQYKL
ATKLLLSKVKHALGFDRIKFMITGAAPMSVETKKYFLSLDMPIIEAYGMSESSGAHSVAK
VHDPSFESIGKTLPGIETKIDNPNEEGHGEICKRGRNVFMGYIGELDKTLEALDDDGWLH
TGDIGYVDENGYLFITGRIKELVITAGGENIPPVHIENLVKAECSAISNAFLVGDNRKFL
TILISLKTEVDKEGAPLDELAPESLKLMKSLNLNYTKLSEVLNAGPDVKVSQAIQDAIVR
ANK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g5144.t6 | Gene3D | G3DSA:3.40.50.12780 | - | 32 | 342 | 2.5E-52 |
| 7 | g5144.t6 | Gene3D | G3DSA:3.40.50.12780 | - | 359 | 498 | 6.3E-37 |
| 2 | g5144.t6 | PANTHER | PTHR43272 | LONG-CHAIN-FATTY-ACID–COA LIGASE | 6 | 603 | 1.0E-212 |
| 3 | g5144.t6 | PANTHER | PTHR43272:SF32 | LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 | 6 | 603 | 1.0E-212 |
| 1 | g5144.t6 | Pfam | PF00501 | AMP-binding enzyme | 41 | 505 | 3.0E-94 |
| 5 | g5144.t6 | ProSitePatterns | PS00455 | Putative AMP-binding domain signature. | 213 | 224 | - |
| 4 | g5144.t6 | SUPERFAMILY | SSF56801 | Acetyl-CoA synthetase-like | 30 | 555 | 1.27E-103 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5144/g5144.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t6.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.
