General information for g10447.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 2-hydroxyacyl-CoA lyase 1.
Parent gene
- The parent gene g10447 is located on chr_1: 9875185..9875542 (- 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_1 | g10447 | g10447.t1 | TTS | g10447.t1 | 9873343 | 9873343 |
| chr_1 | g10447 | g10447.t1 | isoform | g10447.t1 | 9873606 | 9875542 |
| chr_1 | g10447 | g10447.t1 | exon | g10447.t1.exon1 | 9873606 | 9874481 |
| chr_1 | g10447 | g10447.t1 | cds | g10447.t1.CDS1 | 9873606 | 9874481 |
| chr_1 | g10447 | g10447.t1 | exon | g10447.t1.exon2 | 9874541 | 9875202 |
| chr_1 | g10447 | g10447.t1 | cds | g10447.t1.CDS2 | 9874541 | 9875202 |
| chr_1 | g10447 | g10447.t1 | exon | g10447.t1.exon3 | 9875268 | 9875385 |
| chr_1 | g10447 | g10447.t1 | cds | g10447.t1.CDS3 | 9875268 | 9875385 |
| chr_1 | g10447 | g10447.t1 | exon | g10447.t1.exon4 | 9875489 | 9875542 |
| chr_1 | g10447 | g10447.t1 | cds | g10447.t1.CDS4 | 9875489 | 9875542 |
| chr_1 | g10447 | g10447.t1 | TSS | g10447.t1 | 9875640 | 9875640 |
Sequences
>g10447.t1 Gene=g10447 Length=1710
ATGGGTGAAGAAATGGATGGAAATATGATTTTAGCAAAATCATTAAAAGATCAGGGTATT
GAATATGTCTTTGGTATAGTTGGAATACCTGTGATTGAGCTGTCAATGGCTATGCAGAGT
GTTGGACTCAAGTACATTGGCATGAGAAATGAGCAGAGTGCTTGCTATGCAGCTCAAGCA
ATTGGCTACTTAACGAAAAAACCAGGCGTGTGTTTAGTTGTTAGTGGTCCCGGTTTGTTA
CACGTAACAGGTGGAATGGCAAATGCCCAAATCAATTGTTGGCCATTGTTAGTAATTGGA
GGAGCCACTTCTGAAGATCACGAAGGCATAGGAGGTTTTCAAGAATGTCCTCAAGTAGAA
CTCAGTAGACCATACTGCAAATATTCAGCTAGACCACCAAATGCATCTTTAATTCCAACA
CATGTTGAGAAAGCAGTTAGACTTGCAACATATGGTCGACCTGGAGCATGTTATCTTGAT
TTTCCTGGAAATATTTTGCAATCACGTATTAGTGTTGATAAAATTGTAAATTCATATGCT
CATCCAGAGCCACCATTTGTTTTTCCAAATCCCAAAGATGTTATTAGAGCAGTTGATGCA
TTAATGAATGCAAAAAGACCTCTGATTATTATTGGAAAAGGATCTGCTTATGCTAGAGCG
GAGACTTACTTAAGACAACTCGTTCATCAAACTAATTTGCCTTTCTTAGCAACTCCTATG
GGCAAAGGTGTTGTTCCTGATAATGCACGTCAGTGTGTTGGTTCAGCAAGAACAACAGCA
TTACAAAAAGCTGATGTAGTTTTGCTTGTAGGTGCAAGATTAAACTGGATTTTGCACTTT
GGACGTCCACCACGATTTAATGCTGATGTAAAAGTGATTCAAATTGATATTGTTCCTGAA
GAAATGCATAACTCCATTAAGAGTCATATTGCTGTTCAATCAGATATTGTTCCTTTTACA
GACGCATTGATTGATGAGTTTACGAAAAAGAAATTCCGTTTTAATGAAAACAATGAGTGG
TGGAAGGAATTGAACGAAAAATGTGAGAAAAATCAAAAGACTGTGAAAGCAATGCAGTCT
GATGAAAAAGTACCTTTGAACTATTATGCTGTATTTCACAATATTCGTGAAATTATTCCA
TCTGACTGCATCATTGTAAGTGAAGGTGCTAACACAATGGATATAGGTCGTTCAATGCTG
TTAAACAATTTACCTCGTCATCGTTTAGATGCTGGAACATTTGGAACAATGGGAGTTGGA
ATTGGATTTGCTATTGCTGCTGCTTTATATTGTAGAGATTATTGTCCAAGCAAGAGAGTT
GTGTGTGTTGAAGGTGATTCAGCTTTTGGTTTTTCTGGCATGGAAATTGAAACACTTGTG
AGATATTCATTACCAGTGGTAATAGTTATTGTAAATAACAGTGGTATCTATAGTGGATTT
ACGGTTGAAGATTTTAAAAGTTTACAAAATATGGGTGATGCAACTTTAACTACACCACCA
ACTGCCTTGAGCGCAGAGACACGCTATGAAAATATCATGAACATGTTTGGCAAAAAAGGA
TATTTTGTTAGAACAATTCCAGAGTTGCAAAATGCTCTTAGAGAAGCTTTAATCCCATCT
GATCATCCTTCAATCATAAATGTTGCTATTAATCCGCAAGCAGACAGAAAGCCTCAAACG
TACAGCTGGTTGACTGAATCAAAATTGTAA
>g10447.t1 Gene=g10447 Length=569
MGEEMDGNMILAKSLKDQGIEYVFGIVGIPVIELSMAMQSVGLKYIGMRNEQSACYAAQA
IGYLTKKPGVCLVVSGPGLLHVTGGMANAQINCWPLLVIGGATSEDHEGIGGFQECPQVE
LSRPYCKYSARPPNASLIPTHVEKAVRLATYGRPGACYLDFPGNILQSRISVDKIVNSYA
HPEPPFVFPNPKDVIRAVDALMNAKRPLIIIGKGSAYARAETYLRQLVHQTNLPFLATPM
GKGVVPDNARQCVGSARTTALQKADVVLLVGARLNWILHFGRPPRFNADVKVIQIDIVPE
EMHNSIKSHIAVQSDIVPFTDALIDEFTKKKFRFNENNEWWKELNEKCEKNQKTVKAMQS
DEKVPLNYYAVFHNIREIIPSDCIIVSEGANTMDIGRSMLLNNLPRHRLDAGTFGTMGVG
IGFAIAAALYCRDYCPSKRVVCVEGDSAFGFSGMEIETLVRYSLPVVIVIVNNSGIYSGF
TVEDFKSLQNMGDATLTTPPTALSAETRYENIMNMFGKKGYFVRTIPELQNALREALIPS
DHPSIINVAINPQADRKPQTYSWLTESKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g10447.t1 | CDD | cd07035 | TPP_PYR_POX_like | 10 | 162 | 6.54563E-57 |
| 19 | g10447.t1 | CDD | cd02004 | TPP_BZL_OCoD_HPCL | 368 | 550 | 1.79612E-83 |
| 10 | g10447.t1 | Gene3D | G3DSA:3.40.50.970 | - | 2 | 185 | 4.6E-58 |
| 12 | g10447.t1 | Gene3D | G3DSA:3.40.50.1220 | - | 187 | 346 | 5.7E-42 |
| 11 | g10447.t1 | Gene3D | G3DSA:3.40.50.970 | - | 347 | 562 | 3.2E-54 |
| 4 | g10447.t1 | PANTHER | PTHR43710:SF2 | 2-HYDROXYACYL-COA LYASE 1 | 3 | 560 | 3.3E-241 |
| 5 | g10447.t1 | PANTHER | PTHR43710 | 2-HYDROXYACYL-COA LYASE | 3 | 560 | 3.3E-241 |
| 2 | g10447.t1 | Pfam | PF02776 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain | 6 | 171 | 2.0E-45 |
| 3 | g10447.t1 | Pfam | PF00205 | Thiamine pyrophosphate enzyme, central domain | 196 | 323 | 5.9E-32 |
| 1 | g10447.t1 | Pfam | PF02775 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain | 390 | 548 | 1.5E-25 |
| 15 | g10447.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 19 | - |
| 17 | g10447.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 20 | 43 | - |
| 13 | g10447.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 44 | 408 | - |
| 16 | g10447.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 409 | 430 | - |
| 14 | g10447.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 431 | 569 | - |
| 7 | g10447.t1 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 3 | 175 | 2.21E-44 |
| 9 | g10447.t1 | SUPERFAMILY | SSF52467 | DHS-like NAD/FAD-binding domain | 188 | 349 | 6.55E-41 |
| 8 | g10447.t1 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) | 363 | 563 | 8.95E-41 |
| 6 | g10447.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 409 | 431 | - |
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 transcript has been annotated with K12261 (2-hydroxyacyl-CoA lyase)
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.
