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.t7 isoform g9940.t7 6117230 6119674
chr_1 g9940 g9940.t7 exon g9940.t7.exon1 6117230 6117483
chr_1 g9940 g9940.t7 exon g9940.t7.exon2 6117608 6117665
chr_1 g9940 g9940.t7 exon g9940.t7.exon3 6117775 6118134
chr_1 g9940 g9940.t7 exon g9940.t7.exon4 6118209 6118396
chr_1 g9940 g9940.t7 exon g9940.t7.exon5 6118480 6118645
chr_1 g9940 g9940.t7 cds g9940.t7.CDS1 6118558 6118645
chr_1 g9940 g9940.t7 exon g9940.t7.exon6 6118705 6119674
chr_1 g9940 g9940.t7 cds g9940.t7.CDS2 6118705 6119672
chr_1 g9940 g9940.t7 TSS g9940.t7 NA NA
chr_1 g9940 g9940.t7 TTS g9940.t7 NA NA

Sequences

>g9940.t7 Gene=g9940 Length=1996
AATTTATCGGTTAAAAAAATTCAAAAATTCGCAGTCCCCTATTTTCGCATCTTCTATAAG
TTTTTTGTGCCGCTGCTTCATAAAGAAATTTACGATTCTACAATCGATAAAAATTTTTAA
ATAAAAAGTGCTTGAGTTGTTTGCTAATCATTAAAACAAGATAAATCTGTGAAGAAACAT
TGGTTTCATTGAGAAAAACTAAATTGAATCTTTTACTGATAGTGATAAAGGATAAAAATA
AAAGAAAAACATTGGTTTTTGAATACATATATTACTGATTGATTCAACTAACAATATGGC
TGATCCAAAACAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAACCTAA
TCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCGCAAGC
AAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAAAGAAG
AAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATTCGTAT
GAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATTCAATC
ATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACTGTCGA
AGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCG
TCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAA
AGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATTCATTG
TGAAGGAGATCCGATTAAACGAAGAAGAAGAAGCGTTGAATGCTGTCGGTTATGATGATA
TTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATTGCGTC
ATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTATGGAC
CACCAGGTACTGGAAAAACTTTAATTGCAAGAGCTGTAGCAAATGAGACTGGCGCTTTCT
TCTTCTTAATTAATGGTCCTGAGATTATGTCTAAATTAGCTGGTGAATCAGAATCAAATT
TGCGTAAAGCATTCGAAGAAGCAGATAAGAATTCACCTGCAATTATATTTATTGATGAAT
TGGATGCAATTGCTCCTAAGCGTGAAAAAACTCATGGTGAAGTTGAACGCAGAATTGTCT
CTCAATTATTGACTCTCATGGACGGTATGAAGAAAAGCTCTCACGTTATCGTTATTGCTG
CAACAAATCGTCCAAATAGTATCGATCCAGCTCTTCGTCGATTCGGTCGCTTTGATCGTG
AAATTGATATTGGCATTCCAGACGCAACTGGCCGTTTAGAGGTGTTGCGTATTCACACTA
AAAATATGAAATTAGGCGAAGATGTTGATCTTGAACAAATTGCTGCTGAATCGCATGGTC
ATGTTGGCGCTGATTTGGCTTCATTGTGCTCAGAAGCTGCACTTCAACAAATTCGTGAGA
AAATGGATTTGATTGATTTGGAAGACGATCAAATTGATGCCGACGTTTTAAATTCATTGG
CTGTTTCTATGGATAATTTCCGTTATGCTATGACCAAATCAAGTCCATCAGCTTTGCGTG
AAACAGTCGTGGAAACTCCAACAACTACATGGGCCGATATTGGTGGTTTAGAAAATGTCA
AGCGTGAATTACAAGAATTGGTTCAATATCCAGTTGAGCATCCAGATAAATTTTTGAAAT
TTGGTATGCAACCATCACGCGGTGTTCTTTTCTATGGTCCACCCGGTTGTGGTAAAACTT
TGCTCGCTAAAGCAATTGCTAATGAATGTCAGGCTAACTTTATCTCAGTCAAGGGTCCTG
AACTTTTAACTATGTGGTTCGGTGAATCAGAAGCAAATGTTAGAGACATTTTTGATAAAG
CTCGTTCTGCTGCACC

>g9940.t7 Gene=g9940 Length=352
MVELPLRHPSLFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL
AGESESNLRKAFEEADKNSPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGMKKS
SHVIVIAATNRPNSIDPALRRFGRFDREIDIGIPDATGRLEVLRIHTKNMKLGEDVDLEQ
IAAESHGHVGADLASLCSEAALQQIREKMDLIDLEDDQIDADVLNSLAVSMDNFRYAMTK
SSPSALRETVVETPTTTWADIGGLENVKRELQELVQYPVEHPDKFLKFGMQPSRGVLFYG
PPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDKARSAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g9940.t7 CDD cd00009 AAA 11 152 2.02648E-31
14 g9940.t7 CDD cd00009 AAA 262 349 3.77041E-13
11 g9940.t7 Gene3D G3DSA:3.40.50.300 - 1 153 5.6E-62
12 g9940.t7 Gene3D G3DSA:1.10.8.60 - 154 237 6.5E-32
10 g9940.t7 Gene3D G3DSA:3.40.50.300 - 238 352 2.8E-40
4 g9940.t7 PANTHER PTHR23077:SF69 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE 1 352 1.5E-222
5 g9940.t7 PANTHER PTHR23077 AAA-FAMILY ATPASE 1 352 1.5E-222
1 g9940.t7 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 23 152 1.1E-48
3 g9940.t7 Pfam PF17862 AAA+ lid domain 175 216 4.1E-12
2 g9940.t7 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 296 351 2.7E-19
9 g9940.t7 ProSitePatterns PS00674 AAA-protein family signature. 123 141 -
8 g9940.t7 SMART SM00382 AAA_5 19 155 8.2E-24
7 g9940.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 2 224 2.92E-61
6 g9940.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 254 350 3.24E-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