General information for g6701.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as AFG3-like protein 2.
Parent gene
- The parent gene g6701 is located on chr_2: 18111888..18113220 (+ 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 | g6701 | g6701.t12 | isoform | g6701.t12 | 18111610 | 18113220 |
| chr_2 | g6701 | g6701.t12 | exon | g6701.t12.exon1 | 18111610 | 18111626 |
| chr_2 | g6701 | g6701.t12 | exon | g6701.t12.exon2 | 18111683 | 18111816 |
| chr_2 | g6701 | g6701.t12 | cds | g6701.t12.CDS1 | 18111720 | 18111816 |
| chr_2 | g6701 | g6701.t12 | exon | g6701.t12.exon3 | 18111881 | 18113220 |
| chr_2 | g6701 | g6701.t12 | cds | g6701.t12.CDS2 | 18111881 | 18113220 |
| chr_2 | g6701 | g6701.t12 | TTS | g6701.t12 | 18113191 | 18113191 |
| chr_2 | g6701 | g6701.t12 | TSS | g6701.t12 | NA | NA |
Sequences
>g6701.t12 Gene=g6701 Length=1491
GAGTCAAATTTACGTAATGATGTTGCTGGATGTGAAGAAGCTAAGATTGAGATCATGGAA
TTTGTAAATTTTTTGAAAAATCCTCAACAATACATTGACTTGGGTGCAAAAATTCCAAAA
GGTGCTTTGTTAACCGGACCACCTGGCACAGGTAAAACTTTGTTGGCAAAAGCAACTGCA
GGCGAGGCAAATGTTCCATTCATCACTGTTTCTGGTAGTGAATTTTTAGAAATGTTTGTC
GGTGTCGGTCCATCACGAGTTCGTGATATGTTTGCTATGGCACGAAAGCAAGCTCCATGT
ATACTTTTTATTGATGAGATTGATGCAGTTGGTAGAAAGCGTGGTGGCAAATCATTCGGA
GGTCACTCAGAACAAGAAAACACGTTAAATCAGCTTTTAGTAGAGATGGATGGATTTAAT
ACAACAACAAATGTCGTTGTTTTAGCTGCTACAAATCGCTTAGACATATTAGATAAGGCA
TTGCTTAGACCAGGCAGATTCGATCGTCAAATATTTGTTCCTGCGCCTGATATCAAAGGT
CGTGCATCAATTTTCAAAGTACATTTGGCTAATCTTAAAACAGATTTAGATAAAGTTGAA
CTTGCACGAAAAATGGCTGCATTAACTCCTGGTTTCACTGGTGCTGATATTGCTAATGTT
TGTAATGAGGCAGCTTTGATCGCTGCACGCGATTTGAATACATCTATCGTTCTAAAGCAC
TTTGAACAAGCTATTGAACGAGTTATTGCTGGCATGGAGAAAAAAACAAATGTTCTTGCT
CCCGACGAAAAGAGAACTGTAGCATTTCACGAGTCAGGTCATGCTGTATGTGGTTGGTTT
CTTGAACATTCTGATCCGTTACTTAAAGTTTCTATTATTCCACGTGGAAAAGGTCTTGGG
TATGCACAATATCTTCCAAAGGATCAATATCTATTGTCCAAAGAGCAGCTCTACGATAGA
ATGTGTATGACACTTGGTGGACGCGTTGCAGAAGAAATATTTTTTGGAAGAATCACTACA
GGAGCTCAGGATGATTTGAAAAAAGTTACCGAAAGTGCATACTCACAAATTGTGAGATTT
GGTATGAATGAGAAAGTAGGAAAAGTAAGTTTTGACATGTCGCAACCTGGTGATCCTATG
TTTAGTAAGCCTTATTCTGAACAAACGGCACAACTTATTGACGAAGAAGCTCGTGCAATG
ATAAATGAGGCTCATAAAAGAACAACAGAGTTATTATTGAAACATAAAGATGATGTTCAA
AAGGTAGCAGAGCGTTTATTGAAAAATGAAGTTCTCAGTCGTGATGATATGATAGAATTA
CTTGGCAAACGACCATTTGCTGAAAAATCAACATATGAGGAGTTTGTAGAAGGTACTGGT
TCATTTGAAGAAGATACAGCACTTCCATCGGGACTTTCAAGTTGGAATAAAGAGAGAGAG
AAAAAAGAAGAAAGTGAAAATGAAAAAAAAGATGAAAAACAAGAGAAATGA
>g6701.t12 Gene=g6701 Length=478
MEFVNFLKNPQQYIDLGAKIPKGALLTGPPGTGKTLLAKATAGEANVPFITVSGSEFLEM
FVGVGPSRVRDMFAMARKQAPCILFIDEIDAVGRKRGGKSFGGHSEQENTLNQLLVEMDG
FNTTTNVVVLAATNRLDILDKALLRPGRFDRQIFVPAPDIKGRASIFKVHLANLKTDLDK
VELARKMAALTPGFTGADIANVCNEAALIAARDLNTSIVLKHFEQAIERVIAGMEKKTNV
LAPDEKRTVAFHESGHAVCGWFLEHSDPLLKVSIIPRGKGLGYAQYLPKDQYLLSKEQLY
DRMCMTLGGRVAEEIFFGRITTGAQDDLKKVTESAYSQIVRFGMNEKVGKVSFDMSQPGD
PMFSKPYSEQTAQLIDEEARAMINEAHKRTTELLLKHKDDVQKVAERLLKNEVLSRDDMI
ELLGKRPFAEKSTYEEFVEGTGSFEEDTALPSGLSSWNKEREKKEESENEKKDEKQEK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g6701.t12 | CDD | cd00009 | AAA | 21 | 156 | 9.06348E-28 |
| 11 | g6701.t12 | Coils | Coil | Coil | 454 | 478 | - |
| 8 | g6701.t12 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 157 | 1.4E-59 |
| 9 | g6701.t12 | Gene3D | G3DSA:1.10.8.60 | - | 158 | 234 | 1.9E-27 |
| 10 | g6701.t12 | Gene3D | G3DSA:1.20.58.760 | - | 235 | 433 | 4.3E-68 |
| 16 | g6701.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 439 | 478 | - |
| 15 | g6701.t12 | MobiDBLite | mobidb-lite | consensus disorder prediction | 457 | 478 | - |
| 4 | g6701.t12 | PANTHER | PTHR43655 | ATP-DEPENDENT PROTEASE | 1 | 473 | 3.7E-270 |
| 5 | g6701.t12 | PANTHER | PTHR43655:SF7 | AFG3-LIKE PROTEIN 1 | 1 | 473 | 3.7E-270 |
| 1 | g6701.t12 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 25 | 156 | 1.3E-43 |
| 2 | g6701.t12 | Pfam | PF17862 | AAA+ lid domain | 187 | 224 | 4.7E-13 |
| 3 | g6701.t12 | Pfam | PF01434 | Peptidase family M41 | 240 | 421 | 1.8E-65 |
| 13 | g6701.t12 | ProSitePatterns | PS00674 | AAA-protein family signature. | 127 | 145 | - |
| 14 | g6701.t12 | SMART | SM00382 | AAA_5 | 20 | 159 | 2.7E-23 |
| 7 | g6701.t12 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 5 | 250 | 2.79E-63 |
| 6 | g6701.t12 | SUPERFAMILY | SSF140990 | FtsH protease domain-like | 240 | 431 | 1.05E-66 |
| 17 | g6701.t12 | TIGRFAM | TIGR01241 | FtsH_fam: ATP-dependent metallopeptidase HflB | 1 | 423 | 1.6E-187 |
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:0016020 | membrane | CC |
| GO:0006508 | proteolysis | BP |
| GO:0005524 | ATP binding | MF |
| GO:0004222 | metalloendopeptidase activity | MF |
| GO:0004176 | ATP-dependent peptidase activity | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03798 (cell division protease FtsH [EC:3.4.24.-])
Pathway
This gene does not belong to any 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. There were no conditions that were differentially expressed