General information for g5005.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Short-chain specific acyl-CoA dehydrogenase, mitochondrial.
Parent gene
- The parent gene g5005 is located on chr_2: 6398315..6399819 (+ 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_2 | g5005 | g5005.t1 | TSS | g5005.t1 | 6398234 | 6398234 |
| chr_2 | g5005 | g5005.t1 | isoform | g5005.t1 | 6398315 | 6399819 |
| chr_2 | g5005 | g5005.t1 | exon | g5005.t1.exon1 | 6398315 | 6398756 |
| chr_2 | g5005 | g5005.t1 | cds | g5005.t1.CDS1 | 6398315 | 6398756 |
| chr_2 | g5005 | g5005.t1 | exon | g5005.t1.exon2 | 6398921 | 6399003 |
| chr_2 | g5005 | g5005.t1 | cds | g5005.t1.CDS2 | 6398921 | 6399003 |
| chr_2 | g5005 | g5005.t1 | exon | g5005.t1.exon3 | 6399071 | 6399701 |
| chr_2 | g5005 | g5005.t1 | cds | g5005.t1.CDS3 | 6399071 | 6399701 |
| chr_2 | g5005 | g5005.t1 | exon | g5005.t1.exon4 | 6399767 | 6399819 |
| chr_2 | g5005 | g5005.t1 | cds | g5005.t1.CDS4 | 6399767 | 6399819 |
| chr_2 | g5005 | g5005.t1 | TTS | g5005.t1 | 6399985 | 6399985 |
Sequences
>g5005.t1 Gene=g5005 Length=1209
ATGTCTATAAGAAATAAATATTTGTTACATAGTTCTAAGAATATAATCTCAAGATTTTTC
ACTACGAATCTTCCAAATGATGTGATAGTGTTACAAGAATTATGTAGAAAGTTTGCCGAT
ACTGAATTAAAACCTGTTGCAAGTCATCATGATAAAGAAAGTAAATATCCAACTGAACAA
ATTAAGCAGCTTGGTGAAATGGGATTTATGGGAGTAAATGCATCCGTTGAATTCGGTGGT
TCTGGCTTAAAAACTCTTGCACTCTCTGTTATTGTTGAAGAGCTTTCTAGAGGCGATGCA
TCAGTAGGGTCTATTGTATCTATTCATAATTGTCTTTATGCAAATTTAATTGATAGAGTA
GCTAATCAGGCACAAAAAGAACAATGGTTAAGAGAATTTACACAAGGAAAGAAAATTGGA
GCTTTTGCATTAAGTGAAAGTGATGCCGGTTCGGATGTTGCAAATATTTCAACAAAAGCT
GTTAAAGATGGTGATTATTATATTTTAAATGGTACAAAAGCATGGGTCACAAGTGCGGAA
CAAGCTTCTGCAGCTATAATTTTTGCTACTGTCGATAGAGATAAAAAACATAAAGGCATA
GCTGCATTTCTAGTCAGTTTAGATCAACCAGGTGTAGTTGTAGGAAAAAATGAACGAAAA
ATGAGCATTAAAGCTACCTCAACGTGTACTATCACATTAAATGATGTTCATGTTCATTCC
AGTCAACTTTTGTGTAAACCAGGTGAAGGTTTCAGAGTAGCTATGGAGCAACTTGATGTT
GCTCGAATTGGAATTGCTTCACAAGCATTAGGTATCGCTCAAGCTTCTTTGGATACTGCC
ATTGCATATGCAGCTCAACGTATAGCTTTTGATAATCCCATACTAAGATTATCGTCTGTT
AAACAAAGACTTGCAGAAATGGCAACATCAATTGAATCGTCAAGACTTTTAGTACGACAA
GCAGCTCAGAAAAAAGACGAGCATCTACGCTCAACAAAATACACATCAATGGCAAAATGG
CAAGCTAGTCAAACTGCAACATTCTGTGCACATAATTGTATCCAAATCATGGGTGGGATG
GGAATTGTTGAGTCATCTGATGCTGAACGTTACTATCGAGACGCAAGAATAACTGAAATA
TATGGAGGAGTTACAGATGTACAAATAATGATTATTGCTGAGCAGTTACAAAAGGAATAT
GGGCTATGA
>g5005.t1 Gene=g5005 Length=402
MSIRNKYLLHSSKNIISRFFTTNLPNDVIVLQELCRKFADTELKPVASHHDKESKYPTEQ
IKQLGEMGFMGVNASVEFGGSGLKTLALSVIVEELSRGDASVGSIVSIHNCLYANLIDRV
ANQAQKEQWLREFTQGKKIGAFALSESDAGSDVANISTKAVKDGDYYILNGTKAWVTSAE
QASAAIIFATVDRDKKHKGIAAFLVSLDQPGVVVGKNERKMSIKATSTCTITLNDVHVHS
SQLLCKPGEGFRVAMEQLDVARIGIASQALGIAQASLDTAIAYAAQRIAFDNPILRLSSV
KQRLAEMATSIESSRLLVRQAAQKKDEHLRSTKYTSMAKWQASQTATFCAHNCIQIMGGM
GIVESSDAERYYRDARITEIYGGVTDVQIMIIAEQLQKEYGL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g5005.t1 | Gene3D | G3DSA:1.10.540.10 | - | 18 | 139 | 0 |
| 9 | g5005.t1 | Gene3D | G3DSA:2.40.110.10 | - | 140 | 253 | 0 |
| 10 | g5005.t1 | Gene3D | G3DSA:1.20.140.10 | - | 254 | 401 | 0 |
| 4 | g5005.t1 | PANTHER | PTHR43884:SF26 | MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED | 12 | 400 | 0 |
| 5 | g5005.t1 | PANTHER | PTHR43884 | ACYL-COA DEHYDROGENASE | 12 | 400 | 0 |
| 11 | g5005.t1 | PIRSF | PIRSF016578 | PIGM | 31 | 399 | 0 |
| 3 | g5005.t1 | Pfam | PF02771 | Acyl-CoA dehydrogenase, N-terminal domain | 31 | 136 | 0 |
| 1 | g5005.t1 | Pfam | PF02770 | Acyl-CoA dehydrogenase, middle domain | 141 | 236 | 0 |
| 2 | g5005.t1 | Pfam | PF00441 | Acyl-CoA dehydrogenase, C-terminal domain | 248 | 396 | 0 |
| 6 | g5005.t1 | SUPERFAMILY | SSF56645 | Acyl-CoA dehydrogenase NM domain-like | 21 | 259 | 0 |
| 7 | g5005.t1 | SUPERFAMILY | SSF47203 | Acyl-CoA dehydrogenase C-terminal domain-like | 247 | 400 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5005/g5005.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5005.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | MF |
| GO:0050660 | flavin adenine dinucleotide binding | MF |
| GO:0055114 | NA | NA |
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.
