Gene loci information

Transcript annotation

  • This transcript has been annotated as 2-hydroxyacyl-CoA lyase 1.

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 g10447 g10447.t20 TTS g10447.t20 9873343 9873343
chr_1 g10447 g10447.t20 isoform g10447.t20 9873606 9875202
chr_1 g10447 g10447.t20 exon g10447.t20.exon1 9873606 9874481
chr_1 g10447 g10447.t20 cds g10447.t20.CDS1 9873606 9874481
chr_1 g10447 g10447.t20 exon g10447.t20.exon2 9874541 9875202
chr_1 g10447 g10447.t20 cds g10447.t20.CDS2 9874541 9875119
chr_1 g10447 g10447.t20 TSS g10447.t20 9875640 9875640

Sequences

>g10447.t20 Gene=g10447 Length=1538
CTCAAGCAATTGGCTACTTAACGAAAAAACCAGGCGTGTGTTTAGTTGTTAGTGGTCCCG
GTTTGTTACACGTAACAGGTGGAATGGCAAATGCCCAAATCAATTGTTGGCCATTGTTAG
TAATTGGAGGAGCCACTTCTGAAGATCACGAAGGCATAGGAGGTTTTCAAGAATGTCCTC
AAGTAGAACTCAGTAGACCATACTGCAAATATTCAGCTAGACCACCAAATGCATCTTTAA
TTCCAACACATGTTGAGAAAGCAGTTAGACTTGCAACATATGGTCGACCTGGAGCATGTT
ATCTTGATTTTCCTGGAAATATTTTGCAATCACGTATTAGTGTTGATAAAATTGTAAATT
CATATGCTCATCCAGAGCCACCATTTGTTTTTCCAAATCCCAAAGATGTTATTAGAGCAG
TTGATGCATTAATGAATGCAAAAAGACCTCTGATTATTATTGGAAAAGGATCTGCTTATG
CTAGAGCGGAGACTTACTTAAGACAACTCGTTCATCAAACTAATTTGCCTTTCTTAGCAA
CTCCTATGGGCAAAGGTGTTGTTCCTGATAATGCACGTCAGTGTGTTGGTTCAGCAAGAA
CAACAGCATTACAAAAAGCTGATGTAGTTTTGCTTGTAGGTGCAAGATTAAACTGGATTT
TGCACTTTGGACGTCCACCACGATTTAATGCTGATGTAAAAGTGATTCAAATTGATATTG
TTCCTGAAGAAATGCATAACTCCATTAAGAGTCATATTGCTGTTCAATCAGATATTGTTC
CTTTTACAGACGCATTGATTGATGAGTTTACGAAAAAGAAATTCCGTTTTAATGAAAACA
ATGAGTGGTGGAAGGAATTGAACGAAAAATGTGAGAAAAATCAAAAGACTGTGAAAGCAA
TGCAGTCTGATGAAAAAGTACCTTTGAACTATTATGCTGTATTTCACAATATTCGTGAAA
TTATTCCATCTGACTGCATCATTGTAAGTGAAGGTGCTAACACAATGGATATAGGTCGTT
CAATGCTGTTAAACAATTTACCTCGTCATCGTTTAGATGCTGGAACATTTGGAACAATGG
GAGTTGGAATTGGATTTGCTATTGCTGCTGCTTTATATTGTAGAGATTATTGTCCAAGCA
AGAGAGTTGTGTGTGTTGAAGGTGATTCAGCTTTTGGTTTTTCTGGCATGGAAATTGAAA
CACTTGTGAGATATTCATTACCAGTGGTAATAGTTATTGTAAATAACAGTGGTATCTATA
GTGGATTTACGGTTGAAGATTTTAAAAGTTTACAAAATATGGGTGATGCAACTTTAACTA
CACCACCAACTGCCTTGAGCGCAGAGACACGCTATGAAAATATCATGAACATGTTTGGCA
AAAAAGGATATTTTGTTAGAACAATTCCAGAGTTGCAAAATGCTCTTAGAGAAGCTTTAA
TCCCATCTGATCATCCTTCAATCATAAATGTTGCTATTAATCCGCAAGCAGACAGAAAGC
CTCAAACGTACAGCTGGTTGACTGAATCAAAATTGTAA

>g10447.t20 Gene=g10447 Length=484
MANAQINCWPLLVIGGATSEDHEGIGGFQECPQVELSRPYCKYSARPPNASLIPTHVEKA
VRLATYGRPGACYLDFPGNILQSRISVDKIVNSYAHPEPPFVFPNPKDVIRAVDALMNAK
RPLIIIGKGSAYARAETYLRQLVHQTNLPFLATPMGKGVVPDNARQCVGSARTTALQKAD
VVLLVGARLNWILHFGRPPRFNADVKVIQIDIVPEEMHNSIKSHIAVQSDIVPFTDALID
EFTKKKFRFNENNEWWKELNEKCEKNQKTVKAMQSDEKVPLNYYAVFHNIREIIPSDCII
VSEGANTMDIGRSMLLNNLPRHRLDAGTFGTMGVGIGFAIAAALYCRDYCPSKRVVCVEG
DSAFGFSGMEIETLVRYSLPVVIVIVNNSGIYSGFTVEDFKSLQNMGDATLTTPPTALSA
ETRYENIMNMFGKKGYFVRTIPELQNALREALIPSDHPSIINVAINPQADRKPQTYSWLT
ESKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g10447.t20 CDD cd07035 TPP_PYR_POX_like 1 77 2.35014E-23
17 g10447.t20 CDD cd02004 TPP_BZL_OCoD_HPCL 283 465 2.23278E-85
10 g10447.t20 Gene3D G3DSA:3.40.50.970 - 1 100 3.0E-23
12 g10447.t20 Gene3D G3DSA:3.40.50.1220 - 102 261 4.2E-42
11 g10447.t20 Gene3D G3DSA:3.40.50.970 - 262 477 2.2E-54
4 g10447.t20 PANTHER PTHR43710:SF2 2-HYDROXYACYL-COA LYASE 1 1 475 9.7E-196
5 g10447.t20 PANTHER PTHR43710 2-HYDROXYACYL-COA LYASE 1 475 9.7E-196
2 g10447.t20 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain 1 86 1.1E-16
3 g10447.t20 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain 111 238 4.4E-32
1 g10447.t20 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain 305 463 1.1E-25
14 g10447.t20 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 325 -
15 g10447.t20 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 326 346 -
13 g10447.t20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 347 484 -
8 g10447.t20 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding) 1 90 1.62E-16
9 g10447.t20 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain 103 264 4.62E-41
7 g10447.t20 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding) 278 478 6.3E-41
6 g10447.t20 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 324 346 -

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:0000287 magnesium ion binding MF
GO:0003824 catalytic activity MF
GO:0030976 thiamine pyrophosphate binding MF

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