General information for g6545.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Derlin-1.
Parent gene
- The parent gene g6545 is located on chr_2: 17575305..17575805 (+ strand)
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.t1 | TSS | g6545.t1 | 17574793 | 17574793 |
| chr_2 | g6545 | g6545.t1 | isoform | g6545.t1 | 17574826 | 17575695 |
| chr_2 | g6545 | g6545.t1 | exon | g6545.t1.exon1 | 17574826 | 17574978 |
| chr_2 | g6545 | g6545.t1 | cds | g6545.t1.CDS1 | 17574826 | 17574978 |
| chr_2 | g6545 | g6545.t1 | exon | g6545.t1.exon2 | 17575047 | 17575238 |
| chr_2 | g6545 | g6545.t1 | cds | g6545.t1.CDS2 | 17575047 | 17575238 |
| chr_2 | g6545 | g6545.t1 | exon | g6545.t1.exon3 | 17575297 | 17575695 |
| chr_2 | g6545 | g6545.t1 | cds | g6545.t1.CDS3 | 17575297 | 17575695 |
| chr_2 | g6545 | g6545.t1 | TTS | g6545.t1 | 17575799 | 17575799 |
Sequences
>g6545.t1 Gene=g6545 Length=744
ATGTCGGATTTTTCCTCCTGGTATAATTCGATTCCTCGCTTTACGAGATATTATTTAACA
GCAACTGTCGGATTATCGGTAGCGGAAAAGATTGGTCTTGTTTCAAGATATGCACTTTTG
TTAAATTGGCCATTAGTTATATCTCACTTCAATATATGGAGACCAATTACAGCTTTATTC
TACTATCCAACTTCATTTCACTTTCTCATGAACTGCTTTTTCATGTATAATTACTCATCG
CGTCTTGAGAAGGAACATTATTTAGGTAGTCCAAGCGATTTTGTCTACATGCTCCTTTTC
AACTGGATATGTTGTCTAGGTGTTTCACTTTTTGTACCACTTCCAGTTTTAATGGATCCA
ATGGTTTTATCAGTTTTATACATTTGGTGTCAACTTAATAAAGAGATTATTGTAACATTT
TGGTTTGGTAGCAGATTTAAAGCAATGTATCTTCCGTGGGTACTTTTTGCCTTCAATGTT
TTATTATCAAATGGTGGAATGCTTTCACTTTTTGGTATTTTGATCGGACATCTTTACTTT
TTCCTTAAATTTACATATCCACTAGAACTGAATGGGTCAGATTTTTTGAAAACACCTCAA
TTTATAAAGAATTATCTTCCTGATGTTAGACCATCTGGCGTTTTTGGATTTGCACCAGAA
GGCCGAACAACACAACACAATGAACCACAAAGAAGAACTGGTACACTTTTTGGTGGTGCA
GGACATAGATTGGGCAATAATTAA
>g6545.t1 Gene=g6545 Length=247
MSDFSSWYNSIPRFTRYYLTATVGLSVAEKIGLVSRYALLLNWPLVISHFNIWRPITALF
YYPTSFHFLMNCFFMYNYSSRLEKEHYLGSPSDFVYMLLFNWICCLGVSLFVPLPVLMDP
MVLSVLYIWCQLNKEIIVTFWFGSRFKAMYLPWVLFAFNVLLSNGGMLSLFGILIGHLYF
FLKFTYPLELNGSDFLKTPQFIKNYLPDVRPSGVFGFAPEGRTTQHNEPQRRTGTLFGGA
GHRLGNN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g6545.t1 | PANTHER | PTHR11009 | DER1-LIKE PROTEIN, DERLIN | 1 | 230 | 4.4E-75 |
| 3 | g6545.t1 | PANTHER | PTHR11009:SF1 | DERLIN-1 | 1 | 230 | 4.4E-75 |
| 1 | g6545.t1 | Pfam | PF04511 | Der1-like family | 11 | 200 | 1.5E-66 |
| 9 | g6545.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 16 | - |
| 18 | g6545.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 17 | 39 | - |
| 12 | g6545.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 40 | 58 | - |
| 16 | g6545.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 59 | 78 | - |
| 10 | g6545.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 79 | 98 | - |
| 15 | g6545.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 99 | 118 | - |
| 11 | g6545.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 119 | 123 | - |
| 17 | g6545.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 124 | 142 | - |
| 8 | g6545.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 143 | 153 | - |
| 14 | g6545.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 154 | 182 | - |
| 13 | g6545.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 183 | 247 | - |
| 7 | g6545.t1 | SUPERFAMILY | SSF144091 | Rhomboid-like | 9 | 186 | 4.58E-14 |
| 5 | g6545.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 52 | 74 | - |
| 4 | g6545.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 95 | 117 | - |
| 6 | g6545.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 153 | 175 | - |
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 transcript has been annotated with K11519 (Derlin-1)
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.
