Gene loci information

Transcript annotation

  • This transcript has been annotated as Derlin-1.

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_2 g6545 g6545.t3 TSS g6545.t3 17574793 17574793
chr_2 g6545 g6545.t3 isoform g6545.t3 17574826 17575695
chr_2 g6545 g6545.t3 exon g6545.t3.exon1 17574826 17574978
chr_2 g6545 g6545.t3 cds g6545.t3.CDS1 17574826 17574978
chr_2 g6545 g6545.t3 exon g6545.t3.exon2 17575047 17575226
chr_2 g6545 g6545.t3 cds g6545.t3.CDS2 17575047 17575226
chr_2 g6545 g6545.t3 exon g6545.t3.exon3 17575297 17575695
chr_2 g6545 g6545.t3 cds g6545.t3.CDS3 17575297 17575695
chr_2 g6545 g6545.t3 TTS g6545.t3 17575799 17575799

Sequences

>g6545.t3 Gene=g6545 Length=732
ATGTCGGATTTTTCCTCCTGGTATAATTCGATTCCTCGCTTTACGAGATATTATTTAACA
GCAACTGTCGGATTATCGGTAGCGGAAAAGATTGGTCTTGTTTCAAGATATGCACTTTTG
TTAAATTGGCCATTAGTTATATCTCACTTCAATATATGGAGACCAATTACAGCTTTATTC
TACTATCCAACTTCATTTCACTTTCTCATGAACTGCTTTTTCATGTATAATTACTCATCG
CGTCTTGAGAAGGAACATTATTTAGGTAGTCCAAGCGATTTTGTCTACATGCTCCTTTTC
AACTGGATATGTTGTCTAGGTGTTTCACTTTTTGTTTTAATGGATCCAATGGTTTTATCA
GTTTTATACATTTGGTGTCAACTTAATAAAGAGATTATTGTAACATTTTGGTTTGGTAGC
AGATTTAAAGCAATGTATCTTCCGTGGGTACTTTTTGCCTTCAATGTTTTATTATCAAAT
GGTGGAATGCTTTCACTTTTTGGTATTTTGATCGGACATCTTTACTTTTTCCTTAAATTT
ACATATCCACTAGAACTGAATGGGTCAGATTTTTTGAAAACACCTCAATTTATAAAGAAT
TATCTTCCTGATGTTAGACCATCTGGCGTTTTTGGATTTGCACCAGAAGGCCGAACAACA
CAACACAATGAACCACAAAGAAGAACTGGTACACTTTTTGGTGGTGCAGGACATAGATTG
GGCAATAATTAA

>g6545.t3 Gene=g6545 Length=243
MSDFSSWYNSIPRFTRYYLTATVGLSVAEKIGLVSRYALLLNWPLVISHFNIWRPITALF
YYPTSFHFLMNCFFMYNYSSRLEKEHYLGSPSDFVYMLLFNWICCLGVSLFVLMDPMVLS
VLYIWCQLNKEIIVTFWFGSRFKAMYLPWVLFAFNVLLSNGGMLSLFGILIGHLYFFLKF
TYPLELNGSDFLKTPQFIKNYLPDVRPSGVFGFAPEGRTTQHNEPQRRTGTLFGGAGHRL
GNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g6545.t3 PANTHER PTHR11009 DER1-LIKE PROTEIN, DERLIN 1 226 2.9E-73
3 g6545.t3 PANTHER PTHR11009:SF1 DERLIN-1 1 226 2.9E-73
1 g6545.t3 Pfam PF04511 Der1-like family 11 196 5.6E-65
10 g6545.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 16 -
16 g6545.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 17 39 -
8 g6545.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 40 58 -
13 g6545.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 79 -
11 g6545.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 80 98 -
15 g6545.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 99 125 -
9 g6545.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 126 145 -
14 g6545.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 146 176 -
12 g6545.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 177 243 -
7 g6545.t3 SUPERFAMILY SSF144091 Rhomboid-like 9 182 6.41E-14
4 g6545.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 52 74 -
5 g6545.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 113 -
6 g6545.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 149 171 -

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

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.

Raw TPM values