Gene loci information

Transcript annotation

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

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.t6 isoform g9940.t6 6117230 6118893
chr_1 g9940 g9940.t6 exon g9940.t6.exon1 6117230 6117483
chr_1 g9940 g9940.t6 exon g9940.t6.exon2 6117608 6117665
chr_1 g9940 g9940.t6 cds g9940.t6.CDS1 6117649 6117665
chr_1 g9940 g9940.t6 exon g9940.t6.exon3 6117775 6118134
chr_1 g9940 g9940.t6 cds g9940.t6.CDS2 6117775 6118134
chr_1 g9940 g9940.t6 exon g9940.t6.exon4 6118209 6118401
chr_1 g9940 g9940.t6 cds g9940.t6.CDS3 6118209 6118401
chr_1 g9940 g9940.t6 exon g9940.t6.exon5 6118480 6118645
chr_1 g9940 g9940.t6 cds g9940.t6.CDS4 6118480 6118645
chr_1 g9940 g9940.t6 exon g9940.t6.exon6 6118705 6118893
chr_1 g9940 g9940.t6 cds g9940.t6.CDS5 6118705 6118892
chr_1 g9940 g9940.t6 TSS g9940.t6 NA NA
chr_1 g9940 g9940.t6 TTS g9940.t6 NA NA

Sequences

>g9940.t6 Gene=g9940 Length=1220
AATTTATCGGTTAAAAAAATTCAAAAATTCGCAGTCCCCTATTTTCGCATCTTCTATAAG
TTTTTTGTGCCGCTGCTTCATAAAGAAATTTACGATTCTACAATCGATAAAAATTTTTAA
ATAAAAAGTGCTTGAGTTGTTTGCTAATCATTAAAACAAGATAAATCTGTGAAGAAACAT
TGGTTTCATTGAGAAAAACTAAATTGAATCTTTTACTGATAGTGATAAAGGATAAAAATA
AAAGAAAAACATTGGTTTTTGAATACATATATTACTGATTGATTCAACTAACAATATGGC
TGATCCAAAACAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAACCTAA
TCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCGCAAGC
AAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAAAGAAG
AAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATTCGTAT
GAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATTCAATC
ATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACTGTCGA
AGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCG
TCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAA
AGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATTCATTG
TGAAGGAGATCCGATTAAACGTGAAGAAGAAGAAGAAGCGTTGAATGCTGTCGGTTATGA
TGATATTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATT
GCGTCATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTA
TGGACCACCAGGTACTGGAAAAACTTTAATTGCAAGAGCTGTAGCAAATGAGACTGGCGC
TTTCTTCTTCTTAATTAATGGTCCTGAGATTATGTCTAAATTAGCTGGTGAATCAGAATC
AAATTTGCGTAAAGCATTCGAAGAAGCAGATAAGAATTCACCTGCAATTATATTTATTGA
TGAATTGGATGCAATTGCTC

>g9940.t6 Gene=g9940 Length=308
MADPKQGDDLATAILKQKSKPNRLMVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGK
RRKETVCIVLSDDTCPNEKIRMNRVVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDT
VEGLTGNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVI
HCEGDPIKREEEEEALNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGIL
LYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEADKNSPAIIF
IDELDAIA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9940.t6 CDD cd00009 AAA 227 308 0
13 g9940.t6 Gene3D G3DSA:2.40.40.20 - 1 105 0
12 g9940.t6 Gene3D G3DSA:3.10.330.10 - 106 202 0
11 g9940.t6 Gene3D G3DSA:3.40.50.300 - 203 308 0
4 g9940.t6 PANTHER PTHR23077:SF69 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE 5 308 0
5 g9940.t6 PANTHER PTHR23077 AAA-FAMILY ATPASE 5 308 0
3 g9940.t6 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 23 104 0
2 g9940.t6 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 124 188 0
1 g9940.t6 Pfam PF00004 ATPase family associated with various cellular activities (AAA) 239 308 0
9 g9940.t6 SMART SM01073 CDC48_N_2 23 106 0
10 g9940.t6 SMART SM01072 CDC48_2_2 123 189 0
6 g9940.t6 SUPERFAMILY SSF50692 ADC-like 20 103 0
8 g9940.t6 SUPERFAMILY SSF54585 Cdc48 domain 2-like 105 195 0
7 g9940.t6 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 196 307 0

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. There were no conditions that were differentially expressed