General information for g3235.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Succinate–CoA ligase [ADP-forming] subunit beta, mitochondrial .
Parent gene
- The parent gene g3235 is located on chr_3: 23944038..23944729 (+ 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_3 | g3235 | g3235.t9 | TSS | g3235.t9 | 23941831 | 23941831 |
| chr_3 | g3235 | g3235.t9 | isoform | g3235.t9 | 23941885 | 23944729 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon1 | 23941885 | 23941944 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon2 | 23942379 | 23942681 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon3 | 23942755 | 23943339 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon4 | 23943719 | 23943931 |
| chr_3 | g3235 | g3235.t9 | cds | g3235.t9.CDS1 | 23943739 | 23943931 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon5 | 23943995 | 23944206 |
| chr_3 | g3235 | g3235.t9 | cds | g3235.t9.CDS2 | 23943995 | 23944206 |
| chr_3 | g3235 | g3235.t9 | exon | g3235.t9.exon6 | 23944325 | 23944729 |
| chr_3 | g3235 | g3235.t9 | cds | g3235.t9.CDS3 | 23944325 | 23944501 |
| chr_3 | g3235 | g3235.t9 | TTS | g3235.t9 | 23944934 | 23944934 |
Sequences
>g3235.t9 Gene=g3235 Length=1778
ATGAGTTTTCTAACTAGATCAGCAATATTTGCAGGTTCATCCTTAAGAAATGGTGCAAAG
ATTCTCAGTGCCGCACAACAAAAACGTCAATTGAACGTTCAAGAGCACGTTTCGTACTCA
TTTTTAAATGAGGCCGGGATTCCAACACCAAAGTAAGAAAACAAAGAAGAAAAAAGAGTG
TGAGACATAGAGAAGATAATGATAATGATGCATGTTGTTGCTGACTCACAAATCGTAATT
TCCTTATCAGCTGCTATTGATTATATGTTTTCTTTTTTTATTTTTGTTTCACACTAACAA
ATTTAAATCTTATAAGAATGAACGTCATTTCAAAAACAAAACTTAAAAACGTGATAAGGA
AATATTCGGTGTTGCAGGTTCAGCTGAAGAAGCTCAACAGATTGCAAAGGATTTAAATAC
AAAGAATTTAGTTTTAAAAGCTCAAGTTTTGGCTGGTGGTCGTGGAAAAGGTTCGTTTAA
AAATGGTCTCAAAGGCGGTGTCAGAATCGTTTACACACCAGAAGAAGCTAAAGAAATCTC
GGGCAAAATGATAAATCAACTCTTGGTCACAAAACAAACTGGTGCAGCAGGTCGAATCTG
TAACCAAGTTATGGTTGCTGAACGAAAATTCCCAAGACGTGAATTTTATTTTGCTGTGAT
GATGGAACGTGCTTTTAATGGCCCAGTACTTATTGCCTCATCGCAAGGAGGTGTAAATAT
TGAAGAAGTTGCTGCAGAAAATCCAGATGCAATTGTTTATGAACCAATCGATATCAATAA
GGGACTCTCTAAAGATCAAGCAATGAAAATTGCAAGAACAGTAGGTTTAGATGATCATTT
GGAAACAACAACTCAAATGCTTTTGAACTTATATGATTTATTCGTCAAAAAAGATGCTCT
TCTTGTAGAAATTAATCCATATGCTGAAGATGCTGGCGAAACCCGTAAACTTTGCTCTTG
ACGCTAAAATGCGTTTTGATGACAATGCCGAATTCCGTCAAAAAGATTTGTTCGCAAAAC
GTGATTATTCTCAAGAAGATCCAAAAGAAGTTGCAGCTGCAAAATTTGATTTGAATTACA
TCGCTTTAGATGGATCAATTGGTTGCATGGTAAATGGTGCAGGTTTGGCAATGGCTACAA
TGGACATCATTAAATTGCACGGAGGCGATCCCGCAAATTTCTTGGACGTTGGTGGCGGTG
CCACTGCAAATGCTGTCAAGGAGGCCTTCAAAATTATTACTGCAGATCCAAAAGTACATG
TTATCCTCGTTAACATTTTTGGAGGTATTATGCGTTGTGATGTGATTGCTGAAGGTATCA
TTGCTGCAACAAAAGAGCTTAATTTGACTTTACCCATCATTGTGCGTCTTCAGGGTACAA
ATGTCAATGAAGCAAAGGAGCTCATTCGCAAATCAAAATTACGCATTTTACCTAAAGATG
ATCTTGACGAAGCTGCAATGCTTAGCGTTCACTTATCTCAAATTGTACATCTTGCACGCG
AAGCTCATCTCAACGTTTTGTTCGAATTAGATCCAGTTCATCATCATTAAATAAGACGTG
AAAGAATTCGAAAATGATGAATAGGAATTATTCATATGTGTTATACTATTAAATTTAAGA
ATGGTGTTAAATTATTGTCCTTATTTCATCAAACCATACAAAAACAAATATCCACGCTTC
ATCAATCTTATCTGTTTCGCACCAAAATTATTCTTATGTTCATCAACTTCTTTTCTTTGT
GTGTTATTTATGATCTTAGTTTTATCATATAAAAAAAT
>g3235.t9 Gene=g3235 Length=193
MRFDDNAEFRQKDLFAKRDYSQEDPKEVAAAKFDLNYIALDGSIGCMVNGAGLAMATMDI
IKLHGGDPANFLDVGGGATANAVKEAFKIITADPKVHVILVNIFGGIMRCDVIAEGIIAA
TKELNLTLPIIVRLQGTNVNEAKELIRKSKLRILPKDDLDEAAMLSVHLSQIVHLAREAH
LNVLFELDPVHHH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g3235.t9 | Gene3D | G3DSA:3.40.50.261 | - | 25 | 172 | 1.6E-56 |
| 2 | g3235.t9 | PANTHER | PTHR11815:SF10 | SUCCINATE–COA LIGASE [ADP-FORMING] SUBUNIT BETA, MITOCHONDRIAL | 1 | 174 | 1.4E-93 |
| 3 | g3235.t9 | PANTHER | PTHR11815 | SUCCINYL-COA SYNTHETASE BETA CHAIN | 1 | 174 | 1.4E-93 |
| 1 | g3235.t9 | Pfam | PF00549 | CoA-ligase | 47 | 164 | 3.4E-27 |
| 5 | g3235.t9 | ProSitePatterns | PS01217 | ATP-citrate lyase / succinyl-CoA ligases family signature 3. | 42 | 66 | - |
| 4 | g3235.t9 | SUPERFAMILY | SSF52210 | Succinyl-CoA synthetase domains | 24 | 169 | 1.31E-53 |
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:0006099 | tricarboxylic acid cycle | BP |
| GO:0003824 | catalytic activity | 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.
