General information for g11395.t3
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.t3 | isoform | g11395.t3 | 15949995 | 15952952 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon1 | 15949995 | 15950707 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS1 | 15949995 | 15950707 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon2 | 15950770 | 15950854 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS2 | 15950770 | 15950854 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon3 | 15950917 | 15951517 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS3 | 15950917 | 15951517 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon4 | 15951587 | 15951848 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS4 | 15951587 | 15951848 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon5 | 15951901 | 15951975 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS5 | 15951901 | 15951975 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon6 | 15952038 | 15952145 |
| chr_1 | g11395 | g11395.t3 | cds | g11395.t3.CDS6 | 15952038 | 15952101 |
| chr_1 | g11395 | g11395.t3 | exon | g11395.t3.exon7 | 15952884 | 15952952 |
| chr_1 | g11395 | g11395.t3 | TSS | g11395.t3 | 15952963 | 15952963 |
| chr_1 | g11395 | g11395.t3 | TTS | g11395.t3 | NA | NA |
Sequences
>g11395.t3 Gene=g11395 Length=1913
ATAAGTGGAAGTGATGAGTCGTAAAAAACGAGGCTAAGGCATCTCTTGTAATTTATTAAA
TTAAATTTGTGTTTCTGATCATTTTTATTTGACTCATTCTGAAAAAATTAAAAATGGCCA
GTTTGTCGTTTGATGTCAAACAGATTTCTTTAGTTATCTTAATCTTCTTTATGATAAATA
TTGCCCTATGTCAAAATTCACAATTTCAACCACAACCTCGAATTAGACACCAAAGACCGG
GTATTTCAAGAACTCGACCGGTTCAGAGAACAAATCCAAGATTGCACCCATGTGAACAAA
GCAGTTGTTATCCTGCGACAGGTAATCTTCTCATTGGCAGAGAAAACCGTCTAACAGCTT
CATCAACTTGTGGTTTACATGAGCCTGAACGTTTTTGCATTGTGTCACATTTAGAAGACA
AAAAATGTTTCCTTTGTGAAACCAATCAATATACAGAAAATAATTCGCAGCTTAATCATC
GTGTTGGTCAAATAATTTACAAATTTAGACCAGGAACACTGGAAAATACTTGGTGGCAAT
CTGAGAATGGCAAAGAAAATGTCACAATTCAATTGGATCTCGAAGCAGAGTTTCATTTTA
CTCATTTGATTATCGTCTTTGCTACTTTCCGTCCTGCAGCCATGTTGATTGAACGGTCAT
ATGATTTTGGTAAAAGTTGGCATGTTTATCGTTATTTTGCATCAAACTGTGCCGAATCGT
TTCCATTTGCGTTGCGAGAAAGTGAATCGAAAAATATTACTGATGTCACATGCGATCAAC
GCTACTCAAGTGTTGAGCCGTCAAAAAATGGTGAAGTCATTTTCCGAGTACTCCCACCAA
GCATGAATATCGCAAATCCTTATGCTGATCATGTACAAAATATGCTGAAAATGACAAATT
TGAGAATCAATTTTACAAAACTGCATTCGTTAGGTGACACACTTTTAGATGACCGATCAG
AAATACAAGAGAAATACTACTATGCAATTTCCAATATGGTCGTTCGTGGATCATGTTCGT
GCTATGGACATGCATCTCGTTGCTTACCGCTGGACGGTTTTGAAACACAGAACGATATGG
TTCATGGAAGATGTGAATGTACACATCATACCAAGGGATTAAACTGTGAATTTTGTGAAG
ATTTCTTCAATGATCTACCATGGAAACCAGCGCTTGGAAAGCAAACTAATGCTTGCAAAA
AATGTAATTGTAATAATCATGCGACAAGTTGTCATTTTGATCAAGCAGTATATGAACATT
CTGGAAGAGTAAGCGGAGGAGTTTGTGATAATTGTGAACATAATACTCAAGGTCAACATT
GTGAACAATGTATTCCATTCTTCTATCGTGATCCGAATGAAGATATTCAGAGTCCGTATG
CTTGCAAACCTTGTGATTGTGATCCATTAGGTTCACTCGATGATGGAATTTGTGATTCAG
TCTCAGATGCTGAAAGTGAAGTTGAAGCCGGTGCATGTCATTGCAAGAAAAATGTAAAAG
GACGACGATGTGATGTTTGTAAGGAAGGTTTTTGGAATTTAACAGCTGAAAATCCAGATG
GTTGTGAAGAATGCACATGTAATATCTTGGGAACAGTCAATAATTTGGGATGCAATTTTT
ACACTGGCGAGTGTACATGTAAACGATTGGTTATGGGTAAAGATTGTAATCAATGTATGC
CAGAAACTTATGGATTATCAGAAAGCAGAGATGGTTGCACACCTTGTGATTGTGATCCTG
GTGGTTCACTTGACAATAATTGCGATGTTATCACAGGAGAATGTAAATGTCGTCCATATA
TGCAAGGCAGAAACTGCAGTGAACCAAAACAGAATCATTTCATTCCAAATCTTCACATTA
TTGTTGAAGCCGAAGGGCCAAATGCCATTTGTGAAACACAATCATCATATAAT
>g11395.t3 Gene=g11395 Length=600
MASLSFDVKQISLVILIFFMINIALCQNSQFQPQPRIRHQRPGISRTRPVQRTNPRLHPC
EQSSCYPATGNLLIGRENRLTASSTCGLHEPERFCIVSHLEDKKCFLCETNQYTENNSQL
NHRVGQIIYKFRPGTLENTWWQSENGKENVTIQLDLEAEFHFTHLIIVFATFRPAAMLIE
RSYDFGKSWHVYRYFASNCAESFPFALRESESKNITDVTCDQRYSSVEPSKNGEVIFRVL
PPSMNIANPYADHVQNMLKMTNLRINFTKLHSLGDTLLDDRSEIQEKYYYAISNMVVRGS
CSCYGHASRCLPLDGFETQNDMVHGRCECTHHTKGLNCEFCEDFFNDLPWKPALGKQTNA
CKKCNCNNHATSCHFDQAVYEHSGRVSGGVCDNCEHNTQGQHCEQCIPFFYRDPNEDIQS
PYACKPCDCDPLGSLDDGICDSVSDAESEVEAGACHCKKNVKGRRCDVCKEGFWNLTAEN
PDGCEECTCNILGTVNNLGCNFYTGECTCKRLVMGKDCNQCMPETYGLSESRDGCTPCDC
DPGGSLDNNCDVITGECKCRPYMQGRNCSEPKQNHFIPNLHIIVEAEGPNAICETQSSYN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 31 | g11395.t3 | CDD | cd00055 | EGF_Lam | 300 | 352 | 5.16206E-6 |
| 33 | g11395.t3 | CDD | cd00055 | EGF_Lam | 364 | 414 | 8.27368E-6 |
| 32 | g11395.t3 | CDD | cd00055 | EGF_Lam | 426 | 485 | 5.64619E-9 |
| 30 | g11395.t3 | CDD | cd00055 | EGF_Lam | 487 | 536 | 8.61182E-8 |
| 29 | g11395.t3 | CDD | cd00055 | EGF_Lam | 537 | 576 | 4.87463E-9 |
| 19 | g11395.t3 | Gene3D | G3DSA:2.60.120.1490 | - | 50 | 303 | 3.2E-94 |
| 23 | g11395.t3 | Gene3D | G3DSA:2.170.300.10 | - | 304 | 418 | 1.4E-41 |
| 21 | g11395.t3 | Gene3D | G3DSA:2.10.25.10 | Laminin | 425 | 485 | 6.0E-16 |
| 22 | g11395.t3 | Gene3D | G3DSA:2.10.25.10 | Laminin | 486 | 536 | 1.5E-11 |
| 20 | g11395.t3 | Gene3D | G3DSA:2.10.25.10 | Laminin | 537 | 581 | 2.2E-9 |
| 7 | g11395.t3 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 58 | 586 | 1.0E-234 |
| 8 | g11395.t3 | PANTHER | PTHR10574:SF233 | LAMININ SUBUNIT BETA-1 | 58 | 586 | 1.0E-234 |
| 9 | g11395.t3 | PRINTS | PR00011 | Type III EGF-like signature | 448 | 466 | 1.9E-15 |
| 12 | g11395.t3 | PRINTS | PR00011 | Type III EGF-like signature | 500 | 518 | 1.9E-15 |
| 11 | g11395.t3 | PRINTS | PR00011 | Type III EGF-like signature | 521 | 549 | 1.9E-15 |
| 10 | g11395.t3 | PRINTS | PR00011 | Type III EGF-like signature | 550 | 568 | 1.9E-15 |
| 1 | g11395.t3 | Pfam | PF00055 | Laminin N-terminal (Domain VI) | 65 | 299 | 6.0E-78 |
| 4 | g11395.t3 | Pfam | PF00053 | Laminin EGF domain | 301 | 352 | 2.2E-5 |
| 6 | g11395.t3 | Pfam | PF00053 | Laminin EGF domain | 364 | 424 | 5.3E-9 |
| 3 | g11395.t3 | Pfam | PF00053 | Laminin EGF domain | 427 | 484 | 9.1E-12 |
| 5 | g11395.t3 | Pfam | PF00053 | Laminin EGF domain | 487 | 535 | 1.2E-8 |
| 2 | g11395.t3 | Pfam | PF00053 | Laminin EGF domain | 538 | 576 | 7.0E-8 |
| 25 | g11395.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 26 | g11395.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 10 | - |
| 27 | g11395.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 11 | 21 | - |
| 28 | g11395.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 26 | - |
| 24 | g11395.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 600 | - |
| 41 | g11395.t3 | ProSitePatterns | PS01248 | Laminin-type EGF-like (LE) domain signature. | 507 | 540 | - |
| 47 | g11395.t3 | ProSiteProfiles | PS51117 | Laminin N-terminal domain profile. | 61 | 300 | 39.936 |
| 46 | g11395.t3 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 301 | 363 | 11.55 |
| 45 | g11395.t3 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 364 | 426 | 13.625 |
| 44 | g11395.t3 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 427 | 486 | 18.119 |
| 42 | g11395.t3 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 487 | 537 | 15.282 |
| 43 | g11395.t3 | ProSiteProfiles | PS50027 | Laminin-type EGF-like (LE) domain profile. | 538 | 574 | 7.989 |
| 40 | g11395.t3 | SMART | SM00136 | LamNT_2 | 59 | 299 | 1.9E-103 |
| 36 | g11395.t3 | SMART | SM00180 | lamegf_3 | 301 | 361 | 8.0E-5 |
| 39 | g11395.t3 | SMART | SM00180 | lamegf_3 | 364 | 424 | 2.2E-9 |
| 35 | g11395.t3 | SMART | SM00180 | lamegf_3 | 427 | 484 | 6.0E-13 |
| 38 | g11395.t3 | SMART | SM00180 | lamegf_3 | 487 | 535 | 2.3E-8 |
| 37 | g11395.t3 | SMART | SM00180 | lamegf_3 | 538 | 593 | 2.9E-6 |
| 14 | g11395.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 301 | 366 | 6.7E-8 |
| 16 | g11395.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 364 | 416 | 1.34E-10 |
| 15 | g11395.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 451 | 489 | 2.51E-7 |
| 17 | g11395.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 487 | 530 | 1.23E-6 |
| 13 | g11395.t3 | SUPERFAMILY | SSF57196 | EGF/Laminin | 538 | 577 | 1.26E-7 |
| 18 | g11395.t3 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 26 | - |
| 34 | g11395.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 31 | - |
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.
