General information for g11395.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t4 | isoform | g11395.t4 | 15950386 | 15951517 |
| chr_1 | g11395 | g11395.t4 | exon | g11395.t4.exon1 | 15950386 | 15950707 |
| chr_1 | g11395 | g11395.t4 | cds | g11395.t4.CDS1 | 15950388 | 15950707 |
| chr_1 | g11395 | g11395.t4 | exon | g11395.t4.exon2 | 15950770 | 15950854 |
| chr_1 | g11395 | g11395.t4 | cds | g11395.t4.CDS2 | 15950770 | 15950854 |
| chr_1 | g11395 | g11395.t4 | exon | g11395.t4.exon3 | 15950917 | 15951517 |
| chr_1 | g11395 | g11395.t4 | cds | g11395.t4.CDS3 | 15950917 | 15951390 |
| chr_1 | g11395 | g11395.t4 | TSS | g11395.t4 | NA | NA |
| chr_1 | g11395 | g11395.t4 | TTS | g11395.t4 | NA | NA |
Sequences
>g11395.t4 Gene=g11395 Length=1008
AACACTGGAAAATACTTGGTGGCAATCTGAGAATGGCAAAGAAAATGTCACAATTCAATT
GGATCTCGAAGCAGAGTTTCATTTTACTCATTTGATTATCGTCTTTGCTACTTTCCGTCC
TGCAGCCATGTTGATTGAACGGTCATATGATTTTGGTAAAAGTTGGCATGTTTATCGTTA
TTTTGCATCAAACTGTGCCGAATCGTTTCCATTTGCGTTGCGAGAAAGTGAATCGAAAAA
TATTACTGATGTCACATGCGATCAACGCTACTCAAGTGTTGAGCCGTCAAAAAATGGTGA
AGTCATTTTCCGAGTACTCCCACCAAGCATGAATATCGCAAATCCTTATGCTGATCATGT
ACAAAATATGCTGAAAATGACAAATTTGAGAATCAATTTTACAAAACTGCATTCGTTAGG
TGACACACTTTTAGATGACCGATCAGAAATACAAGAGAAATACTACTATGCAATTTCCAA
TATGGTCGTTCGTGGATCATGTTCGTGCTATGGACATGCATCTCGTTGCTTACCGCTGGA
CGGTTTTGAAACACAGAACGATATGGTTCATGGAAGATGTGAATGTACACATCATACCAA
GGGATTAAACTGTGAATTTTGTGAAGATTTCTTCAATGATCTACCATGGAAACCAGCGCT
TGGAAAGCAAACTAATGCTTGCAAAAAATGTAATTGTAATAATCATGCGACAAGTTGTCA
TTTTGATCAAGCAGTATATGAACATTCTGGAAGAGTAAGCGGAGGAGTTTGTGATAATTG
TGAACATAATACTCAAGGTCAACATTGTGAACAATGTATTCCATTCTTCTATCGTGATCC
GAATGAAGATATTCAGAGTCCGTATGCTTGCAAACCTTGTGATTGTGATCCATTAGGTTC
ACTCGATGATGGAATTTGTGATTCAGTCTCAGATGCTGAAAGTGAAGTTGAAGCCGGTGC
ATGTCATTGCAAGAAAAATGTAAAAGGACGACGATGTGATGTTTGTAA
>g11395.t4 Gene=g11395 Length=293
MLIERSYDFGKSWHVYRYFASNCAESFPFALRESESKNITDVTCDQRYSSVEPSKNGEVI
FRVLPPSMNIANPYADHVQNMLKMTNLRINFTKLHSLGDTLLDDRSEIQEKYYYAISNMV
VRGSCSCYGHASRCLPLDGFETQNDMVHGRCECTHHTKGLNCEFCEDFFNDLPWKPALGK
QTNACKKCNCNNHATSCHFDQAVYEHSGRVSGGVCDNCEHNTQGQHCEQCIPFFYRDPNE
DIQSPYACKPCDCDPLGSLDDGICDSVSDAESEVEAGACHCKKNVKGRRCDVC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g11395.t4 | CDD | cd00055 | EGF_Lam | 124 | 176 | 4.83977E-6 |
| 12 | g11395.t4 | CDD | cd00055 | EGF_Lam | 188 | 238 | 9.5452E-6 |
| 14 | g11395.t4 | CDD | cd00055 | EGF_Lam | 250 | 293 | 4.47728E-5 |
| 9 | g11395.t4 | Gene3D | G3DSA:2.60.120.1490 | - | 1 | 127 | 1.6E-47 |
| 11 | g11395.t4 | Gene3D | G3DSA:2.170.300.10 | - | 128 | 242 | 3.9E-42 |
| 10 | g11395.t4 | Gene3D | G3DSA:2.10.25.10 | Laminin | 249 | 293 | 8.8E-9 |
| 5 | g11395.t4 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 1 | 293 | 2.2E-134 |
| 6 | g11395.t4 | PANTHER | PTHR10574:SF233 | LAMININ SUBUNIT BETA-1 | 1 | 293 | 2.2E-134 |
| 1 | g11395.t4 | Pfam | PF00055 | Laminin N-terminal (Domain VI) | 1 | 123 | 2.0E-39 |
| 2 | g11395.t4 | Pfam | PF00053 | Laminin EGF domain | 125 | 176 | 7.8E-6 |
| 4 | g11395.t4 | Pfam | PF00053 | Laminin EGF domain | 188 | 248 | 1.8E-9 |
| 3 | g11395.t4 | Pfam | PF00053 | Laminin EGF domain | 251 | 293 | 1.8E-6 |
| 15 | g11395.t4 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 215 | 251 | - |
| 23 | g11395.t4 | ProSiteProfiles | PS51117 | Laminin N-terminal domain profile. | 1 | 124 | 22.237 |
| 22 | g11395.t4 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 125 | 187 | 11.55 |
| 21 | g11395.t4 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 188 | 250 | 13.625 |
| 20 | g11395.t4 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 251 | 293 | 14.444 |
| 19 | g11395.t4 | SMART | SM00136 | LamNT_2 | 1 | 123 | 2.8E-11 |
| 17 | g11395.t4 | SMART | SM00180 | lamegf_3 | 125 | 185 | 8.0E-5 |
| 18 | g11395.t4 | SMART | SM00180 | lamegf_3 | 188 | 248 | 2.2E-9 |
| 16 | g11395.t4 | SMART | SM00180 | lamegf_3 | 251 | 293 | 0.0046 |
| 8 | g11395.t4 | SUPERFAMILY | SSF57196 | EGF/Laminin | 125 | 190 | 4.6E-8 |
| 7 | g11395.t4 | SUPERFAMILY | SSF57196 | EGF/Laminin | 188 | 240 | 1.38E-10 |
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