Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase.

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_1 g9674 g9674.t5 TSS g9674.t5 4535584 4535584
chr_1 g9674 g9674.t5 isoform g9674.t5 4535665 4536998
chr_1 g9674 g9674.t5 exon g9674.t5.exon1 4535665 4535742
chr_1 g9674 g9674.t5 cds g9674.t5.CDS1 4535665 4535742
chr_1 g9674 g9674.t5 exon g9674.t5.exon2 4535802 4535996
chr_1 g9674 g9674.t5 cds g9674.t5.CDS2 4535802 4535996
chr_1 g9674 g9674.t5 exon g9674.t5.exon3 4536055 4536348
chr_1 g9674 g9674.t5 cds g9674.t5.CDS3 4536055 4536348
chr_1 g9674 g9674.t5 exon g9674.t5.exon4 4536530 4536998
chr_1 g9674 g9674.t5 cds g9674.t5.CDS4 4536530 4536685
chr_1 g9674 g9674.t5 TTS g9674.t5 4537002 4537002

Sequences

>g9674.t5 Gene=g9674 Length=1036
ATGTCAATCAGTCCATTTGTTTATTGGGCTCAAACAGAAGATCAGATTTCTTTAAAAATT
GATCTTAAAGATGTCAAAGATTTCAACATAAAGAGTGACGAAGCAAAATTCAATTTCACA
GGAGTTGGAGTTGGCGCGAGAGGTTTGCAAGAATATAAATTTTCACTAGACTTGTTCAGT
GAAGTCAAATTTGAAGGAATAAAATCAATTAAGACTGACAACAAAGTTGATGTTTTCATA
CCAAAAAAGGAAAAAGGATTTTGGAATCGATTGATTTGTCAACAGCAAAAGCCATCATGG
TTGAAAATTGATTTTGATAGATGGAAGTCAGAAGATATGGACGACGATGATGATGATGAG
AAACCAAGGAATATAATGCAGGATTATCCAGACATGTTTGATCGATTGCAAAAAGAAGAA
CTTGGATTTCGTAGAGAAAATTTCAAGAAAGTTTACTTAATTCTCTACAATTTATTCCAA
TTTGTTGGTTTTACATATATTTTAGTCGTTATGGGAATTCGTTATTCACGTGATGGTGTT
CATTCAATTCCTGGAACTTATGAGGCATATTCCTTGTATGGGCATCAATTGAGATTGTTC
GCTATCCATATTATCTTACACAATTGTTCAAATTTGAAATTGGTTTGCTCACTTGGTTAC
GCTATTCATTATGGATTCCTCTTTATCCGCTTGGTGTTTTATGTGAAGGAATTATTATTT
TGAGAAATATTCCATATTTTGAAGAGACTAAAAGATTGTCAATGACACTGCCTAACAAAT
GGAACTTTACTTTTGATATGCCGACTTTTCTTTATCTTTACATCAGTTTCCTAATTCTTC
CTGGTATAATTTTCATAATGTCTCATATGCAAAAAGTTCGAACCAAAAAACTTGGTGGAC
GAAAGAAAAGCGCTAAATATGATTAAAAATCTTGATTAAAATATTCTTGAATGAATAAGG
ATTTTTTTAAAAGCAAACTTTCAAAATCTGTTTTTGTAACTTGGCTTGTCAATCGATTTT
AATAAAATAAAGAAAA

>g9674.t5 Gene=g9674 Length=240
MSISPFVYWAQTEDQISLKIDLKDVKDFNIKSDEAKFNFTGVGVGARGLQEYKFSLDLFS
EVKFEGIKSIKTDNKVDVFIPKKEKGFWNRLICQQQKPSWLKIDFDRWKSEDMDDDDDDE
KPRNIMQDYPDMFDRLQKEELGFRRENFKKVYLILYNLFQFVGFTYILVVMGIRYSRDGV
HSIPGTYEAYSLYGHQLRLFAIHIILHNCSNLKLVCSLGYAIHYGFLFIRLVFYVKELLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g9674.t5 CDD cd06465 p23_hB-ind1_like 5 111 1.14241E-29
5 g9674.t5 Gene3D G3DSA:2.60.40.790 - 3 125 5.5E-29
2 g9674.t5 PANTHER PTHR22932:SF1 CO-CHAPERONE PROTEIN DAF-41 2 125 1.3E-26
3 g9674.t5 PANTHER PTHR22932 TELOMERASE-BINDING PROTEIN P23 HSP90 CO-CHAPERONE 2 125 1.3E-26
1 g9674.t5 Pfam PF04969 CS domain 7 82 4.2E-4
7 g9674.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 152 -
12 g9674.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 153 175 -
9 g9674.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 176 186 -
11 g9674.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 187 206 -
6 g9674.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 207 217 -
10 g9674.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 235 -
8 g9674.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 240 -
16 g9674.t5 ProSiteProfiles PS51203 CS domain profile. 2 92 14.104
4 g9674.t5 SUPERFAMILY SSF49764 HSP20-like chaperones 1 132 5.68E-26
14 g9674.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 151 173 -
15 g9674.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 212 234 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

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.

Raw TPM values