Gene loci information

Transcript annotation

  • This transcript has been annotated as Very long-chain-fatty-acid–CoA ligase bubblegum.

Parent gene

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.t5 TTS g5144.t5 7274932 7274932
chr_2 g5144 g5144.t5 isoform g5144.t5 7275198 7279047
chr_2 g5144 g5144.t5 exon g5144.t5.exon1 7275198 7275348
chr_2 g5144 g5144.t5 cds g5144.t5.CDS1 7275198 7275348
chr_2 g5144 g5144.t5 exon g5144.t5.exon2 7275405 7275693
chr_2 g5144 g5144.t5 cds g5144.t5.CDS2 7275405 7275693
chr_2 g5144 g5144.t5 exon g5144.t5.exon3 7275762 7275980
chr_2 g5144 g5144.t5 cds g5144.t5.CDS3 7275762 7275980
chr_2 g5144 g5144.t5 exon g5144.t5.exon4 7276044 7276190
chr_2 g5144 g5144.t5 cds g5144.t5.CDS4 7276044 7276190
chr_2 g5144 g5144.t5 exon g5144.t5.exon5 7276246 7276740
chr_2 g5144 g5144.t5 cds g5144.t5.CDS5 7276246 7276740
chr_2 g5144 g5144.t5 exon g5144.t5.exon6 7276800 7277125
chr_2 g5144 g5144.t5 cds g5144.t5.CDS6 7276800 7277125
chr_2 g5144 g5144.t5 exon g5144.t5.exon7 7277185 7277524
chr_2 g5144 g5144.t5 cds g5144.t5.CDS7 7277185 7277519
chr_2 g5144 g5144.t5 exon g5144.t5.exon8 7278845 7279047
chr_2 g5144 g5144.t5 TSS g5144.t5 NA NA

Sequences

>g5144.t5 Gene=g5144 Length=2170
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
ACAAGCCATACAAGACGCAATTGTTCGTGCCAACAAAAGTTCCATTTCCAACGCTCAAAA
AGTTCAAAAGTTTGCATTTTTACCACATGATTTTAGCATTCCTACAGGAGAGTTAGGACC
AACACTTAAAATAAAAAGAAGCTACATCTCAGAAAAGTACAAAGAGATCATCAATAAACT
TTATCATTAG

>g5144.t5 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.t5 Gene3D G3DSA:3.40.50.12780 - 32 342 3.0E-52
7 g5144.t5 Gene3D G3DSA:3.40.50.12780 - 359 498 7.2E-37
2 g5144.t5 PANTHER PTHR43272 LONG-CHAIN-FATTY-ACID–COA LIGASE 6 652 3.2E-238
3 g5144.t5 PANTHER PTHR43272:SF32 LONG-CHAIN-FATTY-ACID–COA LIGASE ACSBG2 6 652 3.2E-238
1 g5144.t5 Pfam PF00501 AMP-binding enzyme 41 505 3.9E-94
5 g5144.t5 ProSitePatterns PS00455 Putative AMP-binding domain signature. 213 224 -
4 g5144.t5 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.t5; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5144.t5.fa.iupred3.txt does not exist

GO terms from InterProScan

There are no GO annotations for this transcript.

KEGG

Orthology

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.

Raw TPM values