General information for g4150.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Glypican-6.
Parent gene
- The parent gene g4150 is located on chr_3: 31008906..31017052 (+ 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 | g4150 | g4150.t1 | isoform | g4150.t1 | 30995433 | 31010611 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon1 | 30995433 | 30995577 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS1 | 30995433 | 30995577 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon2 | 31007695 | 31007929 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS2 | 31007695 | 31007929 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon3 | 31008906 | 31009329 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS3 | 31008906 | 31009329 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon4 | 31009402 | 31009928 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS4 | 31009402 | 31009928 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon5 | 31009988 | 31010136 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS5 | 31009988 | 31010136 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon6 | 31010200 | 31010280 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS6 | 31010200 | 31010280 |
| chr_3 | g4150 | g4150.t1 | exon | g4150.t1.exon7 | 31010340 | 31010611 |
| chr_3 | g4150 | g4150.t1 | cds | g4150.t1.CDS7 | 31010340 | 31010611 |
| chr_3 | g4150 | g4150.t1 | TSS | g4150.t1 | NA | NA |
| chr_3 | g4150 | g4150.t1 | TTS | g4150.t1 | NA | NA |
Sequences
>g4150.t1 Gene=g4150 Length=1833
ATGCCGTCATCGTCAAGCTCGTGTTGTAGCAGTACCATAGAGCAGAGATTATCATATAAT
GCAAAGACAGCTATGGAAAAGGTTACACGCGACTCGATTTATAAAATGTCGTCGACTCTT
CAAACGCGCGCACAAAAATTCAATGAACTCTTTAAAACACTTTTGCAACAGTCCAAAGAA
GGTTTTCATCAGATGTTCAAGCAAACATATGGCGTAATCTATGAGCAAAATTCGTACGTG
TTCAATGACTTATTTACGATGCTTGAGGGCTATTTTATGCGTGGCAAGCTCGATCTTACT
GAGACAATGGATAAATTCTTCAATCAACTATATCAAAAAATGTTCACCGTCATCAATCGG
CAGTATGAATTTAACGATGAATATTTAGCATGTGTTAGCGAATATATGAAAGAATTAAAG
CCATTTGGTGATGTTCCTGATAAGCTCTCTGTTCAAGTTAAACGTTCATTTGTAGCAACG
AGAACTTTTGTTCAGGCACTTACAGCAGCTGCTGAAATTGCAAAAAATATGATGAACTTG
CGACCTTTAAATGAATGTACATCAGCTTTAACAAAAATGTCTTCCTGTGGTGCATGCATG
GGTTACTCTGAAAAACCTTGCGAACTTTACTGTGTAAGTGTCATGAAGCAATGCCTTCAT
CAATATTCAGAGCTTGGTGCTGAGTGGGATAACTTTGTTTTGCAAATGGAAAAAGTTTCG
GATCGTCTTCTTGGCCCCTTCAATATTGTCATGGTCGTTGAGCCAATAAATATTAAAATT
TCTGAAGCAATTATGAATTTCCAGGAGTCAGGTGGAGATATTAGCAAACGTATTTATTCA
GGCTGTGGCACTCCAAAACTTCAAGGCGGCAGACAACGTCGAGCCATTCCATTATTTAAT
ACAAATGCAGATTTATTCATTGATGATGAAGATGATGTGCATCTAAATGAACGTGTGAAG
GTGAAGCGAGCAGCAGATCCTGGCAACCAAGAAAATCGTAGTAGTAGAAATCAAGAGATA
AATGTCAAACCAATTAGTTTTTCACGTAATGACTATCAAGGAAATCGTGGTGGTAGTGGC
AGCAGTAGTAATGGCAATCATCGCGGCAGAAACGGAAACTCAAATAGAAACAATCAACGC
GGTGGTAATTATATGAATGGAAAATCAGACAGTCGAGAATCTGCTCTTGATAAACTTGTA
AAAGAAATTCGACAGAAAGTCAAAGACACGAAAACTTTTTGGACTAATCTACCATACGCA
GCATGCAATAACGATGATTTTGCACCTGCTGGAAATAATGACAATTGTTGGAATGGTCAG
TCCATAAATAGATATGTCGCATCGAATAAAGCAGCACCCGATACACCAGCTAAGCAATCT
CAGATTGTAGCACATCAGTTATTTATTCTGAAAACAACAATCAATCATTTGAAGAATGCA
TATAATGGAAATGATGTCGAATGGCCGGATAGTGATAGTGACGACGGTTCTGATGAATCT
GAATCTGAATCAGGAAGTGGGTCTGGTAGTGGAATTGATGATGAAGATGATGAGGGATCT
GGCATAAGCAAAAATTATCCAGAACAACCAATCACACCGCCCTATAATCCAATTGATACA
TCATCTGAAATTGATAATAATAAAATTGATGGCGATCATATTGGTGCTCAAGCAGATCCG
GACATCACGCAAGAGACAGAAGATGAGTTGACACATAAATCAAGTGCAACATCGACGTGG
AAAACGAAACGACTTATTCTAACATATTTCTTGCCATTAGTGATTTCATGGTTTGGTGGA
TGCATAAGTAGCGCTGTCTCTGAGTTGCTGTGA
>g4150.t1 Gene=g4150 Length=610
MPSSSSSCCSSTIEQRLSYNAKTAMEKVTRDSIYKMSSTLQTRAQKFNELFKTLLQQSKE
GFHQMFKQTYGVIYEQNSYVFNDLFTMLEGYFMRGKLDLTETMDKFFNQLYQKMFTVINR
QYEFNDEYLACVSEYMKELKPFGDVPDKLSVQVKRSFVATRTFVQALTAAAEIAKNMMNL
RPLNECTSALTKMSSCGACMGYSEKPCELYCVSVMKQCLHQYSELGAEWDNFVLQMEKVS
DRLLGPFNIVMVVEPINIKISEAIMNFQESGGDISKRIYSGCGTPKLQGGRQRRAIPLFN
TNADLFIDDEDDVHLNERVKVKRAADPGNQENRSSRNQEINVKPISFSRNDYQGNRGGSG
SSSNGNHRGRNGNSNRNNQRGGNYMNGKSDSRESALDKLVKEIRQKVKDTKTFWTNLPYA
ACNNDDFAPAGNNDNCWNGQSINRYVASNKAAPDTPAKQSQIVAHQLFILKTTINHLKNA
YNGNDVEWPDSDSDDGSDESESESGSGSGSGIDDEDDEGSGISKNYPEQPITPPYNPIDT
SSEIDNNKIDGDHIGAQADPDITQETEDELTHKSSATSTWKTKRLILTYFLPLVISWFGG
CISSAVSELL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4150.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 320 | 393 | - |
| 7 | g4150.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 330 | 390 | - |
| 5 | g4150.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 485 | 519 | - |
| 3 | g4150.t1 | PANTHER | PTHR10822:SF30 | DALLY-LIKE, ISOFORM A | 4 | 571 | 1.7E-144 |
| 4 | g4150.t1 | PANTHER | PTHR10822 | GLYPICAN | 4 | 571 | 1.7E-144 |
| 1 | g4150.t1 | Pfam | PF01153 | Glypican | 6 | 295 | 6.5E-92 |
| 2 | g4150.t1 | Pfam | PF01153 | Glypican | 374 | 543 | 5.7E-20 |
| 8 | g4150.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 584 | - |
| 10 | g4150.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 585 | 606 | - |
| 9 | g4150.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 607 | 610 | - |
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:0062023 | collagen-containing extracellular matrix | CC |
| GO:0046658 | anchored component of plasma membrane | CC |
| GO:0009966 | regulation of signal transduction | BP |
KEGG
Orthology
- This transcript has been annotated with K08110 (glypican 4)
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.
