Gene loci information

Transcript annotation

  • This transcript has been annotated as Elongation of very long chain fatty acids protein.

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_3 g3679 g3679.t19 TSS g3679.t19 27378040 27378040
chr_3 g3679 g3679.t19 isoform g3679.t19 27378330 27380139
chr_3 g3679 g3679.t19 exon g3679.t19.exon1 27378330 27378520
chr_3 g3679 g3679.t19 cds g3679.t19.CDS1 27378431 27378520
chr_3 g3679 g3679.t19 exon g3679.t19.exon2 27378591 27378671
chr_3 g3679 g3679.t19 cds g3679.t19.CDS2 27378591 27378671
chr_3 g3679 g3679.t19 exon g3679.t19.exon3 27379013 27379312
chr_3 g3679 g3679.t19 cds g3679.t19.CDS3 27379013 27379312
chr_3 g3679 g3679.t19 exon g3679.t19.exon4 27379402 27379533
chr_3 g3679 g3679.t19 cds g3679.t19.CDS4 27379402 27379533
chr_3 g3679 g3679.t19 exon g3679.t19.exon5 27379600 27380139
chr_3 g3679 g3679.t19 cds g3679.t19.CDS5 27379600 27379743
chr_3 g3679 g3679.t19 TTS g3679.t19 27380148 27380148

Sequences

>g3679.t19 Gene=g3679 Length=1244
ATGAGCGAACAAATGAATGGCCATTGATTAAATCACCGTTCCCAGGTCTCACAATTATTG
CACTTTATCTATACTTCGTAAATGTGGCTGGACCACGATTTATGAAGGATCGTAAACCTT
TTCAAATGAAGAAAACCTTAATTGTGTATAATTTCCTGCAAGTACTTGTCAGTGTATATC
TTTTCGTAGAGGGCATGAATGGTGGATGGCTTAGACACTACTCTTGGAGATGTCAACCTG
TAGACACATCCAGAAGTGAATTTGGAATGAGAGAAGCACGCGGCTGCTATGTATATTTCA
TTGCCAAACTTACTGAACTCTTGGACACAATTTTCTTTGTACTTCGAAAAAAAGATAATC
AGGTGTCTTTTCTGCATCTGTATCATCACACAGTAATGCCCATGATTTCATGGGGTTGTA
CTAAGTATTTCCCTGGCGGCCATGGTACTTTTATCGGCGTAATTAACTCTTTTGTTCATA
TTGTTATGTACTTTTACTATATGATGGCTGCTATGGGACCTGAATTCCATAAATATTTAT
GGTGGAAACATTGGATCACTAACTTACAAATGATTCAATTCGGTATGGCTTTCTTGCACT
CTGCTCAATTATTATACACAGATTGCGGTTATCCACGCTGGTCTGTCTGCTTCACACTGC
CAAATGCTATCTTTTTCTACATGCTCTTTAACGATTTTTACAAGAAATCATATACGAAGA
AAGGTAAGGGAAAGAAGGTTGCAAATGGAAAAATTAAGCAAGCAAATGGCAAAACAAACG
GTCACATTGTACATGATATCAATCACAACGAAACAAAGCCTGATGAGGATAAAAGAAAAA
GTGAATAGAATTCAAGTTTCAATATAAAGAAGAACAAAATATTTCATATGAGATGATTAC
TGTTTAATAAATAGTAACACAAAGTTTTCTTGCTTTATTTGAAAATGATTTATATTTACT
ACATGTAGTGTTAAAGTACCGACTCTTTTTCAAAATCTAAAGAAAATTTTTTAGGAAGAA
TTCTAAAAATCTTATCTATCTACCTGCATATATACTCCTCTACTTATTTTTAATAAACTA
TAGTAAAATAAGAATTGAAAATTTGTTCTTCAGTGCTATTGAACGCGTGTGATTACTATT
AATCATGAAAAAACTTTCTACCCTAAGTGACTAAAATAGTAATTTAAATGATATTCTGTT
GTGTGTATTTGTTTTGAATGTGCAATAAACTTTCATCAATCAAC

>g3679.t19 Gene=g3679 Length=248
MKDRKPFQMKKTLIVYNFLQVLVSVYLFVEGMNGGWLRHYSWRCQPVDTSRSEFGMREAR
GCYVYFIAKLTELLDTIFFVLRKKDNQVSFLHLYHHTVMPMISWGCTKYFPGGHGTFIGV
INSFVHIVMYFYYMMAAMGPEFHKYLWWKHWITNLQMIQFGMAFLHSAQLLYTDCGYPRW
SVCFTLPNAIFFYMLFNDFYKKSYTKKGKGKKVANGKIKQANGKTNGHIVHDINHNETKP
DEDKRKSE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g3679.t19 MobiDBLite mobidb-lite consensus disorder prediction 229 248 -
8 g3679.t19 MobiDBLite mobidb-lite consensus disorder prediction 230 248 -
2 g3679.t19 PANTHER PTHR11157 FATTY ACID ACYL TRANSFERASE-RELATED 1 212 1.7E-122
3 g3679.t19 PANTHER PTHR11157:SF153 ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN 1 212 1.7E-122
1 g3679.t19 Pfam PF01151 GNS1/SUR4 family 1 211 3.2E-57
10 g3679.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
18 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
14 g3679.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 62 -
21 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 63 81 -
11 g3679.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 82 92 -
22 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 93 110 -
16 g3679.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 115 -
17 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 133 -
13 g3679.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 134 144 -
20 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 165 -
15 g3679.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 166 176 -
19 g3679.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 177 196 -
12 g3679.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 197 248 -
7 g3679.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 13 32 -
6 g3679.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 110 132 -
4 g3679.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 145 167 -
5 g3679.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 196 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC

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. There were no conditions that were differentially expressed