General information for g9940.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transitional endoplasmic reticulum ATPase TER94.
Parent gene
- The parent gene g9940 is located on chr_1: 6119674..6120493 (+ 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 | g9940 | g9940.t1 | TSS | g9940.t1 | 6117534 | 6117534 |
| chr_1 | g9940 | g9940.t1 | isoform | g9940.t1 | 6117649 | 6120493 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon1 | 6117649 | 6117665 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS1 | 6117649 | 6117665 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon2 | 6117775 | 6118134 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS2 | 6117775 | 6118134 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon3 | 6118209 | 6118401 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS3 | 6118209 | 6118401 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon4 | 6118480 | 6118645 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS4 | 6118480 | 6118645 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon5 | 6118705 | 6120003 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS5 | 6118705 | 6120003 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon6 | 6120063 | 6120187 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS6 | 6120063 | 6120187 |
| chr_1 | g9940 | g9940.t1 | exon | g9940.t1.exon7 | 6120251 | 6120493 |
| chr_1 | g9940 | g9940.t1 | cds | g9940.t1.CDS7 | 6120251 | 6120493 |
| chr_1 | g9940 | g9940.t1 | TTS | g9940.t1 | 6120807 | 6120807 |
Sequences
>g9940.t1 Gene=g9940 Length=2403
ATGGCTGATCCAAAACAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAA
CCTAATCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCG
CAAGCAAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAA
AGAAGAAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATT
CGTATGAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATT
CAATCATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACT
GTCGAAGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCT
TATCGTCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAA
TTTAAAGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATT
CATTGTGAAGGAGATCCGATTAAACGTGAAGAAGAAGAAGAAGCGTTGAATGCTGTCGGT
TATGATGATATTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTA
CCATTGCGTCATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTG
TTGTATGGACCACCAGGTACTGGAAAAACTTTAATTGCAAGAGCTGTAGCAAATGAGACT
GGCGCTTTCTTCTTCTTAATTAATGGTCCTGAGATTATGTCTAAATTAGCTGGTGAATCA
GAATCAAATTTGCGTAAAGCATTCGAAGAAGCAGATAAGAATTCACCTGCAATTATATTT
ATTGATGAATTGGATGCAATTGCTCCTAAGCGTGAAAAAACTCATGGTGAAGTTGAACGC
AGAATTGTCTCTCAATTATTGACTCTCATGGACGGTATGAAGAAAAGCTCTCACGTTATC
GTTATTGCTGCAACAAATCGTCCAAATAGTATCGATCCAGCTCTTCGTCGATTCGGTCGC
TTTGATCGTGAAATTGATATTGGCATTCCAGACGCAACTGGCCGTTTAGAGGTGTTGCGT
ATTCACACTAAAAATATGAAATTAGGCGAAGATGTTGATCTTGAACAAATTGCTGCTGAA
TCGCATGGTCATGTTGGCGCTGATTTGGCTTCATTGTGCTCAGAAGCTGCACTTCAACAA
ATTCGTGAGAAAATGGATTTGATTGATTTGGAAGACGATCAAATTGATGCCGACGTTTTA
AATTCATTGGCTGTTTCTATGGATAATTTCCGTTATGCTATGACCAAATCAAGTCCATCA
GCTTTGCGTGAAACAGTCGTGGAAACTCCAACAACTACATGGGCCGATATTGGTGGTTTA
GAAAATGTCAAGCGTGAATTACAAGAATTGGTTCAATATCCAGTTGAGCATCCAGATAAA
TTTTTGAAATTTGGTATGCAACCATCACGCGGTGTTCTTTTCTATGGTCCACCCGGTTGT
GGTAAAACTTTGCTCGCTAAAGCAATTGCTAATGAATGTCAGGCTAACTTTATCTCAGTC
AAGGGTCCTGAACTTTTAACTATGTGGTTCGGTGAATCAGAAGCAAATGTTAGAGACATT
TTTGATAAAGCTCGTTCTGCTGCACCATGTGTTTTGTTCTTTGATGAATTGGACAGTATT
GCTAAATCTCGCGGAGGCAATGTCGGTGATGCAGGTGGAGCTGCTGACAGAGTTATTAAT
CAAATTTTGACTGAAATGGATGGTATGGGAGCCAAGAAAAATGTCTTCATTATTGGTGCA
ACAAATCGTCCTGACATCATCGATAGCGCTATTCTTCGTCCTGGTCGTCTAGATCAGTTG
ATTTATATTCCATTGCCCGATGAAAAATCACGCATTGCTATTTTGCAATCTAACTTGCGC
AAGAGTCCAGTCGGTAAAGAAGTCGACTTGGGATATATTGCAAAAGTCACAAATGGTTTC
TCAGGTGCAGATCTTACAGAAATTTGCCAACGTGCTTGCAAACTTGCAATTCGTCAAGCA
ATCGAAACTGAAATTCGTCGTGAAAAAGCACGAAGTGATAATCAGAATGTTGCAATGGAT
ATGGACGATGATGATCCAGTTCCAGAAATTACACGAGCTCACTTTGAGGAAGCAATGAAA
TTTGCTCGCCGATCCGTATCAGATAATGACATTCGTAAATATGAAATGTTTGCTCAAACT
CTGCAGCAATCGCGAGGATTTGGCAACTCATTCAGATTTCCAGCGGGTTCTGCTGGTTCA
CAAAATCCAGATCAGCAAAATCAACCGAGTAATAACGATCCTGATGATGATCTTTACAGT
TAA
>g9940.t1 Gene=g9940 Length=800
MADPKQGDDLATAILKQKSKPNRLMVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGK
RRKETVCIVLSDDTCPNEKIRMNRVVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDT
VEGLTGNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVI
HCEGDPIKREEEEEALNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGIL
LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIF
IDELDAIAPKREKTHGEVERRIVSQLLTLMDGMKKSSHVIVIAATNRPNSIDPALRRFGR
FDREIDIGIPDATGRLEVLRIHTKNMKLGEDVDLEQIAAESHGHVGADLASLCSEAALQQ
IREKMDLIDLEDDQIDADVLNSLAVSMDNFRYAMTKSSPSALRETVVETPTTTWADIGGL
ENVKRELQELVQYPVEHPDKFLKFGMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISV
KGPELLTMWFGESEANVRDIFDKARSAAPCVLFFDELDSIAKSRGGNVGDAGGAADRVIN
QILTEMDGMGAKKNVFIIGATNRPDIIDSAILRPGRLDQLIYIPLPDEKSRIAILQSNLR
KSPVGKEVDLGYIAKVTNGFSGADLTEICQRACKLAIRQAIETEIRREKARSDNQNVAMD
MDDDDPVPEITRAHFEEAMKFARRSVSDNDIRKYEMFAQTLQQSRGFGNSFRFPAGSAGS
QNPDQQNQPSNNDPDDDLYS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 21 | g9940.t1 | CDD | cd00009 | AAA | 205 | 368 | 1.14916E-30 |
| 20 | g9940.t1 | CDD | cd00009 | AAA | 478 | 645 | 2.51862E-30 |
| 17 | g9940.t1 | Gene3D | G3DSA:2.40.40.20 | - | 2 | 105 | 2.5E-46 |
| 16 | g9940.t1 | Gene3D | G3DSA:3.10.330.10 | - | 106 | 202 | 1.2E-48 |
| 15 | g9940.t1 | Gene3D | G3DSA:3.40.50.300 | - | 203 | 368 | 1.1E-65 |
| 18 | g9940.t1 | Gene3D | G3DSA:1.10.8.60 | - | 370 | 465 | 8.7E-32 |
| 14 | g9940.t1 | Gene3D | G3DSA:3.40.50.300 | - | 466 | 646 | 6.9E-72 |
| 19 | g9940.t1 | Gene3D | G3DSA:1.10.8.60 | - | 647 | 762 | 2.6E-44 |
| 28 | g9940.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 768 | 800 | - |
| 8 | g9940.t1 | PANTHER | PTHR23077:SF69 | TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE | 5 | 779 | 0.0 |
| 9 | g9940.t1 | PANTHER | PTHR23077 | AAA-FAMILY ATPASE | 5 | 779 | 0.0 |
| 7 | g9940.t1 | Pfam | PF02359 | Cell division protein 48 (CDC48), N-terminal domain | 23 | 104 | 4.1E-21 |
| 4 | g9940.t1 | Pfam | PF02933 | Cell division protein 48 (CDC48), domain 2 | 124 | 188 | 1.1E-9 |
| 3 | g9940.t1 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 239 | 368 | 4.8E-48 |
| 5 | g9940.t1 | Pfam | PF17862 | AAA+ lid domain | 391 | 432 | 1.2E-11 |
| 2 | g9940.t1 | Pfam | PF00004 | ATPase family associated with various cellular activities (AAA) | 512 | 645 | 2.2E-45 |
| 6 | g9940.t1 | Pfam | PF17862 | AAA+ lid domain | 668 | 708 | 1.1E-10 |
| 1 | g9940.t1 | Pfam | PF09336 | Vps4 C terminal oligomerisation domain | 724 | 759 | 6.2E-6 |
| 23 | g9940.t1 | ProSitePatterns | PS00674 | AAA-protein family signature. | 339 | 357 | - |
| 22 | g9940.t1 | ProSitePatterns | PS00674 | AAA-protein family signature. | 615 | 633 | - |
| 24 | g9940.t1 | SMART | SM01073 | CDC48_N_2 | 23 | 106 | 4.5E-27 |
| 27 | g9940.t1 | SMART | SM01072 | CDC48_2_2 | 123 | 189 | 1.6E-12 |
| 26 | g9940.t1 | SMART | SM00382 | AAA_5 | 235 | 371 | 8.2E-24 |
| 25 | g9940.t1 | SMART | SM00382 | AAA_5 | 508 | 647 | 3.9E-24 |
| 10 | g9940.t1 | SUPERFAMILY | SSF50692 | ADC-like | 20 | 103 | 9.82E-28 |
| 13 | g9940.t1 | SUPERFAMILY | SSF54585 | Cdc48 domain 2-like | 105 | 195 | 3.92E-34 |
| 12 | g9940.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 200 | 440 | 6.14E-65 |
| 11 | g9940.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 470 | 760 | 5.68E-75 |
| 29 | g9940.t1 | TIGRFAM | TIGR01243 | CDC48: AAA family ATPase, CDC48 subfamily | 28 | 762 | 5.3E-247 |
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:0016787 | hydrolase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K13525 (transitional endoplasmic reticulum ATPase)
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.
