General information for g2360.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Low-density lipoprotein receptor-related protein 5.
Parent gene
- The parent gene g2360 is located on chr_3: 17187024..17188976 (+ 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_3 | g2360 | g2360.t2 | TSS | g2360.t2 | 17179776 | 17179776 |
| chr_3 | g2360 | g2360.t2 | isoform | g2360.t2 | 17180183 | 17183892 |
| chr_3 | g2360 | g2360.t2 | exon | g2360.t2.exon1 | 17180183 | 17180261 |
| chr_3 | g2360 | g2360.t2 | cds | g2360.t2.CDS1 | 17180183 | 17180261 |
| chr_3 | g2360 | g2360.t2 | exon | g2360.t2.exon2 | 17183243 | 17183892 |
| chr_3 | g2360 | g2360.t2 | cds | g2360.t2.CDS2 | 17183243 | 17183892 |
| chr_3 | g2360 | g2360.t2 | TTS | g2360.t2 | NA | NA |
Sequences
>g2360.t2 Gene=g2360 Length=729
ATGAAAAAACTCTGCAATTCATACAATTCGTTAGTGATTTTACTGTTCCTTCTCACCATA
ATCAATATCAATGGAGCAAATGCTGGGCAACCGATAACATTACGAAACTCACCTACTTCA
CATGCATCCTCAATATCAACGACGTCGTCGTCATCATCAACCCTTCTCATATTCACAACA
TATCACGATATTCGCATAGCGAATTTGTCACGTAATCATGTCACCAGCATTACAACAATT
ACAAAGGACTTGGTTGAAGGAGCGGGTCTCGACTTTTATTATGACAAGCAATTGGTATGT
TGGACGGATCAGGGAATGGAAGCAATTCAATGTAAAAAAATGAATGCATCATTTTATGGT
GATCATCAGCCCGTTGGACCGGTGGGAATTGACGAGTTGACAGAAAACATTGACAAGATT
AGCATAATTACCAAACGAATTGAGAAACCTGAGGGAATCGCAATTGATTGGTATACAGAC
AAAATTTACTGGGTTGATGGTGAACTTAATAATATTGAAGTGACAACATTAAATGGAAAA
TATCGCAAGTTGCTTTTCTGGACAGATCTCGATCAGCCAAGGGCAATTTCACTTGTGCCC
GCGCAGAAGCTAATGATATGGTGTGACTGGGGAGAAATTCCTCGAATTGAACGAGCCTCG
ATGGACGGGGATAAGTATAGTCGCATGATTCTCGTTAGCGATCGTATTTATTGGCCAAAT
GGACTCACG
>g2360.t2 Gene=g2360 Length=243
MKKLCNSYNSLVILLFLLTIININGANAGQPITLRNSPTSHASSISTTSSSSSTLLIFTT
YHDIRIANLSRNHVTSITTITKDLVEGAGLDFYYDKQLVCWTDQGMEAIQCKKMNASFYG
DHQPVGPVGIDELTENIDKISIITKRIEKPEGIAIDWYTDKIYWVDGELNNIEVTTLNGK
YRKLLFWTDLDQPRAISLVPAQKLMIWCDWGEIPRIERASMDGDKYSRMILVSDRIYWPN
GLT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g2360.t2 | Gene3D | G3DSA:2.120.10.30 | TolB | 50 | 243 | 3.5E-51 |
| 3 | g2360.t2 | PANTHER | PTHR46513:SF24 | LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN | 51 | 243 | 1.6E-46 |
| 4 | g2360.t2 | PANTHER | PTHR46513 | VITELLOGENIN RECEPTOR-LIKE PROTEIN-RELATED-RELATED | 51 | 243 | 1.6E-46 |
| 2 | g2360.t2 | Pfam | PF00058 | Low-density lipoprotein receptor repeat class B | 160 | 196 | 1.8E-6 |
| 1 | g2360.t2 | Pfam | PF00058 | Low-density lipoprotein receptor repeat class B | 207 | 243 | 9.2E-6 |
| 10 | g2360.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 28 | - |
| 11 | g2360.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 12 | g2360.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 21 | - |
| 13 | g2360.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 28 | - |
| 9 | g2360.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 29 | 243 | - |
| 19 | g2360.t2 | ProSiteProfiles | PS51120 | LDL-receptor class B (LDLRB) repeat profile. | 115 | 159 | 5.422 |
| 18 | g2360.t2 | ProSiteProfiles | PS51120 | LDL-receptor class B (LDLRB) repeat profile. | 160 | 202 | 13.289 |
| 20 | g2360.t2 | ProSiteProfiles | PS51120 | LDL-receptor class B (LDLRB) repeat profile. | 203 | 243 | 11.664 |
| 17 | g2360.t2 | SMART | SM00135 | LY_2 | 77 | 119 | 9.2 |
| 16 | g2360.t2 | SMART | SM00135 | LY_2 | 140 | 182 | 1.9E-10 |
| 15 | g2360.t2 | SMART | SM00135 | LY_2 | 183 | 226 | 7.6E-4 |
| 5 | g2360.t2 | SUPERFAMILY | SSF63825 | YWTD domain | 56 | 243 | 1.7E-21 |
| 7 | g2360.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 28 | - |
| 6 | g2360.t2 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 28 | - |
| 14 | g2360.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
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. There were no conditions that were differentially expressed