Gene loci information

Transcript annotation

  • This transcript has been annotated as Transitional endoplasmic reticulum ATPase TER94.

Parent gene

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.t14 TSS g9940.t14 6117534 6117534
chr_1 g9940 g9940.t14 isoform g9940.t14 6117649 6119674
chr_1 g9940 g9940.t14 exon g9940.t14.exon1 6117649 6118134
chr_1 g9940 g9940.t14 cds g9940.t14.CDS1 6117830 6118134
chr_1 g9940 g9940.t14 exon g9940.t14.exon2 6118209 6118401
chr_1 g9940 g9940.t14 cds g9940.t14.CDS2 6118209 6118401
chr_1 g9940 g9940.t14 exon g9940.t14.exon3 6118480 6118645
chr_1 g9940 g9940.t14 cds g9940.t14.CDS3 6118480 6118645
chr_1 g9940 g9940.t14 exon g9940.t14.exon4 6118705 6119674
chr_1 g9940 g9940.t14 cds g9940.t14.CDS4 6118705 6119672
chr_1 g9940 g9940.t14 TTS g9940.t14 NA NA

Sequences

>g9940.t14 Gene=g9940 Length=1815
ATGGCTGATCCAAAACAGTGAGTATTAAAGTGATAAATATTGAAAAAATAGCCTAAAAAT
GAGTGTCCTAAAAATTTCATAATTTGACTTTATAATTATCTTTGTTTCAATGTCTTAATA
AAACAGAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAACCTAATCGTTT
GATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCGCAAGCAAAAAT
GGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAAAGAAGAAAGGA
GACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATTCGTATGAATCG
TGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATTCAATCATGTCC
TGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACTGTCGAAGGTCT
GACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCGTCCTAT
TCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAAAGTTGT
TGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATTCATTGTGAAGG
AGATCCGATTAAACGTGAAGAAGAAGAAGAAGCGTTGAATGCTGTCGGTTATGATGATAT
TGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATTGCGTCA
TCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTATGGACC
ACCAGGTACTGGAAAAACTTTAATTGCAAGAGCTGTAGCAAATGAGACTGGCGCTTTCTT
CTTCTTAATTAATGGTCCTGAGATTATGTCTAAATTAGCTGGTGAATCAGAATCAAATTT
GCGTAAAGCATTCGAAGAAGCAGATAAGAATTCACCTGCAATTATATTTATTGATGAATT
GGATGCAATTGCTCCTAAGCGTGAAAAAACTCATGGTGAAGTTGAACGCAGAATTGTCTC
TCAATTATTGACTCTCATGGACGGTATGAAGAAAAGCTCTCACGTTATCGTTATTGCTGC
AACAAATCGTCCAAATAGTATCGATCCAGCTCTTCGTCGATTCGGTCGCTTTGATCGTGA
AATTGATATTGGCATTCCAGACGCAACTGGCCGTTTAGAGGTGTTGCGTATTCACACTAA
AAATATGAAATTAGGCGAAGATGTTGATCTTGAACAAATTGCTGCTGAATCGCATGGTCA
TGTTGGCGCTGATTTGGCTTCATTGTGCTCAGAAGCTGCACTTCAACAAATTCGTGAGAA
AATGGATTTGATTGATTTGGAAGACGATCAAATTGATGCCGACGTTTTAAATTCATTGGC
TGTTTCTATGGATAATTTCCGTTATGCTATGACCAAATCAAGTCCATCAGCTTTGCGTGA
AACAGTCGTGGAAACTCCAACAACTACATGGGCCGATATTGGTGGTTTAGAAAATGTCAA
GCGTGAATTACAAGAATTGGTTCAATATCCAGTTGAGCATCCAGATAAATTTTTGAAATT
TGGTATGCAACCATCACGCGGTGTTCTTTTCTATGGTCCACCCGGTTGTGGTAAAACTTT
GCTCGCTAAAGCAATTGCTAATGAATGTCAGGCTAACTTTATCTCAGTCAAGGGTCCTGA
ACTTTTAACTATGTGGTTCGGTGAATCAGAAGCAAATGTTAGAGACATTTTTGATAAAGC
TCGTTCTGCTGCACC

>g9940.t14 Gene=g9940 Length=544
MVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGKRRKETVCIVLSDDTCPNEKIRMNR
VVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDTVEGLTGNIFDVYLKPYFLEAYRPI
HKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVIHCEGDPIKREEEEEALNAVGYDDI
GGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFF
FLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREKTHGEVERRIVS
QLLTLMDGMKKSSHVIVIAATNRPNSIDPALRRFGRFDREIDIGIPDATGRLEVLRIHTK
NMKLGEDVDLEQIAAESHGHVGADLASLCSEAALQQIREKMDLIDLEDDQIDADVLNSLA
VSMDNFRYAMTKSSPSALRETVVETPTTTWADIGGLENVKRELQELVQYPVEHPDKFLKF
GMQPSRGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKA
RSAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g9940.t14 CDD cd00009 AAA 203 344 9.61441E-31
21 g9940.t14 CDD cd00009 AAA 454 541 4.49875E-13
19 g9940.t14 Gene3D G3DSA:2.40.40.20 - 1 81 3.3E-37
18 g9940.t14 Gene3D G3DSA:3.10.330.10 - 82 178 6.5E-49
17 g9940.t14 Gene3D G3DSA:3.40.50.300 - 179 344 5.3E-66
20 g9940.t14 Gene3D G3DSA:1.10.8.60 - 346 438 5.0E-32
16 g9940.t14 Gene3D G3DSA:3.40.50.300 - 439 544 1.5E-38
6 g9940.t14 PANTHER PTHR23077:SF69 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE 1 544 0.0
7 g9940.t14 PANTHER PTHR23077 AAA-FAMILY ATPASE 1 544 0.0
5 g9940.t14 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 2 80 2.3E-20
3 g9940.t14 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 100 164 6.7E-10
1 g9940.t14 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 215 344 2.5E-48
4 g9940.t14 Pfam PF17862 AAA+ lid domain 367 408 7.4E-12
2 g9940.t14 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 488 543 5.0E-19
15 g9940.t14 ProSitePatterns PS00674 AAA-protein family signature. 315 333 -
12 g9940.t14 SMART SM01073 CDC48_N_2 2 82 2.1E-23
14 g9940.t14 SMART SM01072 CDC48_2_2 99 165 1.6E-12
13 g9940.t14 SMART SM00382 AAA_5 211 347 8.2E-24
8 g9940.t14 SUPERFAMILY SSF50692 ADC-like 1 79 1.49E-25
11 g9940.t14 SUPERFAMILY SSF54585 Cdc48 domain 2-like 81 171 2.16E-34
10 g9940.t14 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 176 416 2.52E-65
9 g9940.t14 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 446 542 6.81E-30

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:0005524 ATP binding MF
GO:0016887 ATP hydrolysis 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.

Raw TPM values