General information for g11395.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Laminin subunit beta-1.
Parent gene
- The parent gene g11395 is located on chr_1: 15951601..15952952 (- 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_1 | g11395 | g11395.t2 | isoform | g11395.t2 | 15944776 | 15946940 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon1 | 15944776 | 15945595 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS1 | 15945456 | 15945595 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon2 | 15945683 | 15945827 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS2 | 15945683 | 15945827 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon3 | 15945922 | 15946110 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS3 | 15945922 | 15946110 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon4 | 15946185 | 15946253 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS4 | 15946185 | 15946253 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon5 | 15946316 | 15946388 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS5 | 15946316 | 15946388 |
| chr_1 | g11395 | g11395.t2 | exon | g11395.t2.exon6 | 15946456 | 15946940 |
| chr_1 | g11395 | g11395.t2 | cds | g11395.t2.CDS6 | 15946456 | 15946493 |
| chr_1 | g11395 | g11395.t2 | TSS | g11395.t2 | NA | NA |
| chr_1 | g11395 | g11395.t2 | TTS | g11395.t2 | NA | NA |
Sequences
>g11395.t2 Gene=g11395 Length=1781
TGTGGTAAATGTGGTGGCATTTCATGTGAAAAAGGTGCGCTAACAAAAGCAGAAACAGCA
CTACAATATGCCAAAGACACAGAGAAAATTATAAAAGAGAAAGATCAACAAGCAGAAGAG
CTCATAAGAAAGGTATCGCATGCTAAAACTGAGGCAGTTGAGGCTCATAAAAAGGCAAAA
GAAACATTTGACAAGGTTGAAGAAACATATAATTCTACAGAAACATTACTCAACGAGGGA
CGAGAATTAATTACAAATTTGACAAATATTATTGCAAATAACACTGCCTCGCCTGTGGAA
ATTAAAGATATTGCCGAAAATATTTTGAAGCTTGATTTGCACTTGGATCCATCAGAAATT
AAACATTTGGCTAATAACATTGATAAAACTGTTGCTGAATTAGAGAATGTCGATGATATT
ATTGATAATACTCGTCATGATTTAGAAATGGTTGAAAAACTTAAAACAAGTGCCACTGAA
GCACAAAAGCGTGCTAATGATGTTTTAAAGAGAGCGACTGAAGTTAGTAAAGCATTAGAA
GAAGCCGAAGCGTCTCAGAATGCTGCTAGAGTTGCGATTAAAAAGGCAAACGATGACATA
GCATCTGCAAAATCTGATTTAGAAGATATAAACGATGATGCAACAAAAGCTAGAGCTAGT
GTAGATGAAACGGCAGCCGCTGTTGATGCTTTACAAACAAAATTAAATAAGTTACAGAGG
AAGTTTTTGAAGAACTCACATGATGCAAAAGAGGTGAAGACTCAAGCAGATGTAGCAAAG
GATCTTTCATCTGTAACACACGAGAAAGCGAAAAAGTTAAAGAATCAATACAAATACGCT
AATGACACTTTGAATTCAAAAGCTCAATCTACAGAGTATGCACGAAACAAAGCACAACAA
TTATTGCAGCGAGCTTCAAAAATAACAGTCGACACGAACAATAAATTGAAGGAATTGCGA
GATATGGTGAGCATAACAACATCAAATGACGACGAGTTGGTAGAAATGGAACGAAAAATT
TTGAGACTTAACGGCGAAATCGATGTCTATATACAGCGTATCAGAGACCATGCCGATCGT
TACCGAACTTGCACTTCTTGAAGAAACAAAATATAAAAGATTAAACAAACAATTTTTCCT
AATTGATAGAATCAACTTAATATATTTATAGATAAATCTCTATATTTTTAAAGATGTTCA
ATAGACTTGCCAGTGCCAAATTCTTAAGCGTTAAGAAATCACTTAAAGAGAATTCATTAT
TTCATACTAAAAAAAATTAAAGCACCTACCTTTGCTTAGGGAAAATGAGAAGAGTAAAAA
AAATTCTTAATTAAATGCAAAAAAAACACCGCCATAGTACATATTTTTAATTAATTAATA
ATTTTAAATTCCTAATTACTTAAATCTTTATATGAACTTTTTTATATGTGTTCCGAAAAT
CGTGTGAAAATTAAGTAGAGAAAAAAAATAATTGTAATAAGTAAGTACCAAATAGGAAAT
GCACATCTTATTGACATATAATAATATGTATCAGAGAAAATCGGAAATAAATTGACAACA
GATAAAAATTATGTAATATTTTGCTATTTCTTTTCTTCTTAGCTCCGCTAAATAACAAGT
ATTTCTTTATGCATATAGCGAGAGTTTCTTTTTGCATGTTTTAAGCAACAGCAGTAAATT
GATTTTCAACCGAAACCTTCTTGAAGCAATGAAACGTTGAAACATCGATACAAAAACAAT
CTTTTGGAAGAAAAAAAAAGTTGAGCCATTCACTTGAGTTA
>g11395.t2 Gene=g11395 Length=217
MVEKLKTSATEAQKRANDVLKRATEVSKALEEAEASQNAARVAIKKANDDIASAKSDLED
INDDATKARASVDETAAAVDALQTKLNKLQRKFLKNSHDAKEVKTQADVAKDLSSVTHEK
AKKLKNQYKYANDTLNSKAQSTEYARNKAQQLLQRASKITVDTNNKLKELRDMVSITTSN
DDELVEMERKILRLNGEIDVYIQRIRDHADRYRTCTS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g11395.t2 | Coils | Coil | Coil | 2 | 22 | - |
| 5 | g11395.t2 | Coils | Coil | Coil | 30 | 64 | - |
| 7 | g11395.t2 | Coils | Coil | Coil | 72 | 92 | - |
| 4 | g11395.t2 | Coils | Coil | Coil | 184 | 204 | - |
| 1 | g11395.t2 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 3 | 215 | 4.8E-18 |
| 2 | g11395.t2 | PANTHER | PTHR10574:SF233 | LAMININ SUBUNIT BETA-1 | 3 | 215 | 4.8E-18 |
| 3 | g11395.t2 | SUPERFAMILY | SSF58104 | Methyl-accepting chemotaxis protein (MCP) signaling domain | 10 | 210 | 8.11E-5 |
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.
