General information for g2360.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
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.t4 | isoform | g2360.t4 | 17187024 | 17188976 |
| chr_3 | g2360 | g2360.t4 | exon | g2360.t4.exon1 | 17187024 | 17188976 |
| chr_3 | g2360 | g2360.t4 | cds | g2360.t4.CDS1 | 17187777 | 17188469 |
| chr_3 | g2360 | g2360.t4 | TSS | g2360.t4 | NA | NA |
| chr_3 | g2360 | g2360.t4 | TTS | g2360.t4 | NA | NA |
Sequences
>g2360.t4 Gene=g2360 Length=1953
GGTGAGTGTGGGTGTAACTGTGTATATTTTGGCAGATTTTAATTAATTTTATTTACAGAA
AAATTTTAACAAGCAGCAACATAAATCAAGTTCATTCAATAGCAGCATTTCCAAATGTCA
TCTACTGGTTAGATGAGAAATATGGTTTAGAAAAAGCCACACTTGATGGTGATTTTATAA
AATTGGAGAAAAAATATAATCATCTCACAGATATTGTTGCCGTATGGCATCCTGAGTCGA
AGATAATCAAAAATCATTTGTGTATGTCATCAAGAAATAAATGTACACACATTTGCATAG
CAACACTTAATAACAGTAAAGCAGATGAATTTTGTTCATGTCCAGCTGGATTGATGTTAC
TAAAAGATAAAAAGAGTTGTACAGCACAACCAGTTTGTGGTCCAGATCACTTTACATGTG
CTTCACCATACACAAGTAATGGTTATTCAGGAGATAATAAAGATTGTATTCCTTATGCAT
GGAGATGTAAGTAATTTGAAATCTTCCTCATATAATTTTAATTAATTTTTTTTTATTTCT
AAAGGCGATGGACAAAATGATTGTCCTGATAAATCTGATGAAATGGATTGCCCATCATGC
AGTTCTGATCAATTTCGGTAATTATTTAAAATTAAATTAAATCTTACAAACTTTTGATAA
TATTCATTTTTTAGTTGTAATACAGGAGAATGCATTGATAAAAGTTTTCTTTGTGATGGA
ACTACTCATTGTGCAGATGGTGGTGATGAAGCAATGTGCTGCAATCCAGGAGATTTTCAA
TGTGCAAGCAACCATGTTTGCATACCAAACACATTTATGTGTGACGGTTGGGAACATTGT
GCTGATGGCTCAGATGAGATTAATGAAATTTGTAGCGTAGTTACAAGAAAACCTCCACCA
ACTGACAAAAAATTGTTTGTAGTAATTCTCATAGTTTTGGTGCTTATAATTTTCTTTGTC
GTATATATTTTGCAAATATGTCGAAATAAATTTGCTGATACAATTCGTGAGCCAAAGGAA
GATCAAGCATCAGCTCCGCTATCTCCAGGAGCATTAAACAGTTTGCGAATGACGAAAATT
TCATCAGTAGCGGATGCTGTGAGATTAACGACAATGAGTCGAAACAGCATGAACAGCTAC
GATCGAAATAACATTACTGGAGCGAGCAGTTCAACTACAAACGGAAGTCTAATTGGATAT
CCGAGTAATCCACCGCCATCGCCAGCCACGACCTCAACACTGCACAACAGTTACCCGTAT
AAACATTATAAAGTGATTAATCAAGCTCCACCCACGACACCTTGCAGTACAGATGTTTGT
GAATCAGATTCAAATTATACACCAATATCAGTCAAAAGTTCAAAGCGATCAGCAGATAGT
TGCTATGGTGTAAACATCTATATGGGCAGTAGTTTAAATGGAAGTAGCAACAATAAATCA
TACTAATTTTAATTTAAGATTTCTTCTTTTACATAAATTGTGATAAATTGAGCGAAAGAG
ATGATTTTCCTCAATATAAGTACTTAAAAAATTTTTTGCCAATAATCTTCTTTTTATTGT
GAGAAACCTGATGCAATCAAAAACTGAAATACAATCATGTGCCAATTTTATTAAAAATTG
AAAATCAAAATTTTGAAGAGAAAAAACATTTTATAAATTAAAATACACTTCACAAAAAAA
GTAGTTAAAAAATTTCTTATTACAATCAAATGCCAAAACAAATACCCCTTTAGTTGATAG
ATTTGTAGAATATTATCTAGATGTTATGAGTATTTAGAATGAATATATGCATTTAAGTGC
CTCAGAAATAAAAAAAAAATAAGATAAAAGGATGAGCTTAAAATTTGTGAAATTAAAGAA
TCAATTTTTTGATAGTTAAATCCATTAGTTCAGGAATAATAGTTTTATGTAAATACGAAT
GTGAAATTATTGAAGAAAAAATAAAGAAAGACT
>g2360.t4 Gene=g2360 Length=230
MCCNPGDFQCASNHVCIPNTFMCDGWEHCADGSDEINEICSVVTRKPPPTDKKLFVVILI
VLVLIIFFVVYILQICRNKFADTIREPKEDQASAPLSPGALNSLRMTKISSVADAVRLTT
MSRNSMNSYDRNNITGASSSTTNGSLIGYPSNPPPSPATTSTLHNSYPYKHYKVINQAPP
TTPCSTDVCESDSNYTPISVKSSKRSADSCYGVNIYMGSSLNGSSNNKSY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2360.t4 | CDD | cd00112 | LDLa | 3 | 37 | 3.80709E-10 |
| 5 | g2360.t4 | Gene3D | G3DSA:4.10.400.10 | - | 1 | 56 | 2.7E-12 |
| 2 | g2360.t4 | PANTHER | PTHR46513:SF24 | LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN | 1 | 194 | 3.6E-40 |
| 3 | g2360.t4 | PANTHER | PTHR46513 | VITELLOGENIN RECEPTOR-LIKE PROTEIN-RELATED-RELATED | 1 | 194 | 3.6E-40 |
| 1 | g2360.t4 | Pfam | PF00057 | Low-density lipoprotein receptor domain class A | 3 | 38 | 2.1E-8 |
| 6 | g2360.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 53 | - |
| 8 | g2360.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 73 | - |
| 7 | g2360.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 74 | 230 | - |
| 11 | g2360.t4 | ProSitePatterns | PS01209 | LDL-receptor class A (LDLRA) domain signature. | 16 | 40 | - |
| 13 | g2360.t4 | ProSiteProfiles | PS50068 | LDL-receptor class A (LDLRA) domain profile. | 2 | 41 | 12.312 |
| 12 | g2360.t4 | SMART | SM00192 | LDLa_2 | 2 | 42 | 7.7E-10 |
| 4 | g2360.t4 | SUPERFAMILY | SSF57424 | LDL receptor-like module | 2 | 43 | 3.01E-10 |
| 10 | g2360.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 54 | 76 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
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.
