Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t4 TSS g6545.t4 17574793 17574793
chr_2 g6545 g6545.t4 isoform g6545.t4 17574826 17575695
chr_2 g6545 g6545.t4 exon g6545.t4.exon1 17574826 17575238
chr_2 g6545 g6545.t4 cds g6545.t4.CDS1 17575017 17575238
chr_2 g6545 g6545.t4 exon g6545.t4.exon2 17575297 17575695
chr_2 g6545 g6545.t4 cds g6545.t4.CDS2 17575297 17575695
chr_2 g6545 g6545.t4 TTS g6545.t4 17575799 17575799

Sequences

>g6545.t4 Gene=g6545 Length=812
ATGTCGGATTTTTCCTCCTGGTATAATTCGATTCCTCGCTTTACGAGATATTATTTAACA
GCAACTGTCGGATTATCGGTAGCGGAAAAGATTGGTCTTGTTTCAAGATATGCACTTTTG
TTAAATTGGCCATTAGTTATATCTCACTTCAATGTAAGTGAAGAATTATTGCTTACCTTA
TAAATTAATCTATGAATTTTAAATATTTGTTTTCTTTGCAGATATGGAGACCAATTACAG
CTTTATTCTACTATCCAACTTCATTTCACTTTCTCATGAACTGCTTTTTCATGTATAATT
ACTCATCGCGTCTTGAGAAGGAACATTATTTAGGTAGTCCAAGCGATTTTGTCTACATGC
TCCTTTTCAACTGGATATGTTGTCTAGGTGTTTCACTTTTTGTACCACTTCCAGTTTTAA
TGGATCCAATGGTTTTATCAGTTTTATACATTTGGTGTCAACTTAATAAAGAGATTATTG
TAACATTTTGGTTTGGTAGCAGATTTAAAGCAATGTATCTTCCGTGGGTACTTTTTGCCT
TCAATGTTTTATTATCAAATGGTGGAATGCTTTCACTTTTTGGTATTTTGATCGGACATC
TTTACTTTTTCCTTAAATTTACATATCCACTAGAACTGAATGGGTCAGATTTTTTGAAAA
CACCTCAATTTATAAAGAATTATCTTCCTGATGTTAGACCATCTGGCGTTTTTGGATTTG
CACCAGAAGGCCGAACAACACAACACAATGAACCACAAAGAAGAACTGGTACACTTTTTG
GTGGTGCAGGACATAGATTGGGCAATAATTAA

>g6545.t4 Gene=g6545 Length=206
MNFKYLFSLQIWRPITALFYYPTSFHFLMNCFFMYNYSSRLEKEHYLGSPSDFVYMLLFN
WICCLGVSLFVPLPVLMDPMVLSVLYIWCQLNKEIIVTFWFGSRFKAMYLPWVLFAFNVL
LSNGGMLSLFGILIGHLYFFLKFTYPLELNGSDFLKTPQFIKNYLPDVRPSGVFGFAPEG
RTTQHNEPQRRTGTLFGGAGHRLGNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g6545.t4 PANTHER PTHR11009 DER1-LIKE PROTEIN, DERLIN 8 189 1.9E-62
3 g6545.t4 PANTHER PTHR11009:SF1 DERLIN-1 8 189 1.9E-62
1 g6545.t4 Pfam PF04511 Der1-like family 9 159 8.4E-55
10 g6545.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 11 -
13 g6545.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 33 -
8 g6545.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 34 52 -
15 g6545.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 53 75 -
11 g6545.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 76 80 -
14 g6545.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 81 101 -
9 g6545.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 102 112 -
16 g6545.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 141 -
12 g6545.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 142 206 -
7 g6545.t4 SUPERFAMILY SSF144091 Rhomboid-like 6 145 7.32E-11
6 g6545.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
5 g6545.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 76 -
4 g6545.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 112 134 -

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