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.t4 isoform g9940.t4 6117230 6118649
chr_1 g9940 g9940.t4 exon g9940.t4.exon1 6117230 6117483
chr_1 g9940 g9940.t4 exon g9940.t4.exon2 6117608 6117665
chr_1 g9940 g9940.t4 cds g9940.t4.CDS1 6117649 6117665
chr_1 g9940 g9940.t4 exon g9940.t4.exon3 6117775 6118134
chr_1 g9940 g9940.t4 cds g9940.t4.CDS2 6117775 6118134
chr_1 g9940 g9940.t4 exon g9940.t4.exon4 6118209 6118401
chr_1 g9940 g9940.t4 cds g9940.t4.CDS3 6118209 6118401
chr_1 g9940 g9940.t4 exon g9940.t4.exon5 6118480 6118649
chr_1 g9940 g9940.t4 cds g9940.t4.CDS4 6118480 6118647
chr_1 g9940 g9940.t4 TSS g9940.t4 NA NA
chr_1 g9940 g9940.t4 TTS g9940.t4 NA NA

Sequences

>g9940.t4 Gene=g9940 Length=1035
AATTTATCGGTTAAAAAAATTCAAAAATTCGCAGTCCCCTATTTTCGCATCTTCTATAAG
TTTTTTGTGCCGCTGCTTCATAAAGAAATTTACGATTCTACAATCGATAAAAATTTTTAA
ATAAAAAGTGCTTGAGTTGTTTGCTAATCATTAAAACAAGATAAATCTGTGAAGAAACAT
TGGTTTCATTGAGAAAAACTAAATTGAATCTTTTACTGATAGTGATAAAGGATAAAAATA
AAAGAAAAACATTGGTTTTTGAATACATATATTACTGATTGATTCAACTAACAATATGGC
TGATCCAAAACAAGGAGATGATTTAGCTACAGCAATTTTAAAGCAAAAGTCTAAACCTAA
TCGTTTGATGGTCGATGATGCTACAAATGATGATAACTCAATTGTTTGTCTATCGCAAGC
AAAAATGGACGAGTTGCAATTGTTTCGCGGAGATACAGTTTTGTTAAAGGGGAAAAGAAG
AAAGGAGACTGTTTGTATTGTTTTATCTGACGATACATGTCCTAATGAGAAAATTCGTAT
GAATCGTGTTGTTCGTAACAATTTGCGTGTTCGACTCTCGGATATTGTCGCCATTCAATC
ATGTCCTGATGTTAAATATGGCAAACGTGTTCATATTTTGCCAATTGATGACACTGTCGA
AGGTCTGACTGGCAATATCTTTGATGTTTATTTGAAACCATACTTCCTCGAAGCTTATCG
TCCTATTCATAAAGACGATACTTTTATTGTTCGTGGTGGCATGAGAGCTGTTGAATTTAA
AGTTGTTGGAACAGATCCTGAACCATATTGTATAGTTGCTCCCGATACTGTAATTCATTG
TGAAGGAGATCCGATTAAACGTGAAGAAGAAGAAGAAGCGTTGAATGCTGTCGGTTATGA
TGATATTGGTGGTTGTCGAAAGCAATTGGCTCAAATTAAAGAAATGGTCGAGTTACCATT
GCGTCATCCATCACTTTTCAAAGCAATTGGTGTTAAACCTCCACGAGGTATTTTGTTGTA
TGGACCACCAGGTAA

>g9940.t4 Gene=g9940 Length=246
MADPKQGDDLATAILKQKSKPNRLMVDDATNDDNSIVCLSQAKMDELQLFRGDTVLLKGK
RRKETVCIVLSDDTCPNEKIRMNRVVRNNLRVRLSDIVAIQSCPDVKYGKRVHILPIDDT
VEGLTGNIFDVYLKPYFLEAYRPIHKDDTFIVRGGMRAVEFKVVGTDPEPYCIVAPDTVI
HCEGDPIKREEEEEALNAVGYDDIGGCRKQLAQIKEMVELPLRHPSLFKAIGVKPPRGIL
LYGPPG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g9940.t4 Gene3D G3DSA:2.40.40.20 - 1 105 0
11 g9940.t4 Gene3D G3DSA:3.10.330.10 - 106 201 0
10 g9940.t4 Gene3D G3DSA:3.40.50.300 - 202 246 0
3 g9940.t4 PANTHER PTHR23077:SF69 TRANSITIONAL ENDOPLASMIC RETICULUM ATPASE 5 246 0
4 g9940.t4 PANTHER PTHR23077 AAA-FAMILY ATPASE 5 246 0
2 g9940.t4 Pfam PF02359 Cell division protein 48 (CDC48), N-terminal domain 23 104 0
1 g9940.t4 Pfam PF02933 Cell division protein 48 (CDC48), domain 2 124 188 0
8 g9940.t4 SMART SM01073 CDC48_N_2 23 106 0
9 g9940.t4 SMART SM01072 CDC48_2_2 123 189 0
5 g9940.t4 SUPERFAMILY SSF50692 ADC-like 20 103 0
7 g9940.t4 SUPERFAMILY SSF54585 Cdc48 domain 2-like 105 195 0
6 g9940.t4 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 186 246 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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