Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Laminin subunit beta-1.

Parent gene

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.t7 isoform g11395.t7 15951512 15952101
chr_1 g11395 g11395.t7 exon g11395.t7.exon1 15951512 15951517
chr_1 g11395 g11395.t7 cds g11395.t7.CDS1 15951514 15951517
chr_1 g11395 g11395.t7 exon g11395.t7.exon2 15951587 15951848
chr_1 g11395 g11395.t7 cds g11395.t7.CDS2 15951587 15951848
chr_1 g11395 g11395.t7 exon g11395.t7.exon3 15951901 15951975
chr_1 g11395 g11395.t7 cds g11395.t7.CDS3 15951901 15951975
chr_1 g11395 g11395.t7 exon g11395.t7.exon4 15952038 15952101
chr_1 g11395 g11395.t7 cds g11395.t7.CDS4 15952038 15952101
chr_1 g11395 g11395.t7 TSS g11395.t7 15952963 15952963
chr_1 g11395 g11395.t7 TTS g11395.t7 NA NA

Sequences

>g11395.t7 Gene=g11395 Length=407
ATGGCCAGTTTGTCGTTTGATGTCAAACAGATTTCTTTAGTTATCTTAATCTTCTTTATG
ATAAATATTGCCCTATGTCAAAATTCACAATTTCAACCACAACCTCGAATTAGACACCAA
AGACCGGGTATTTCAAGAACTCGACCGGTTCAGAGAACAAATCCAAGATTGCACCCATGT
GAACAAAGCAGTTGTTATCCTGCGACAGGTAATCTTCTCATTGGCAGAGAAAACCGTCTA
ACAGCTTCATCAACTTGTGGTTTACATGAGCCTGAACGTTTTTGCATTGTGTCACATTTA
GAAGACAAAAAATGTTTCCTTTGTGAAACCAATCAATATACAGAAAATAATTCGCAGCTT
AATCATCGTGTTGGTCAAATAATTTACAAATTTAGACCAGGAACACT

>g11395.t7 Gene=g11395 Length=135
MASLSFDVKQISLVILIFFMINIALCQNSQFQPQPRIRHQRPGISRTRPVQRTNPRLHPC
EQSSCYPATGNLLIGRENRLTASSTCGLHEPERFCIVSHLEDKKCFLCETNQYTENNSQL
NHRVGQIIYKFRPGT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11395.t7 Gene3D G3DSA:2.60.120.1490 - 50 135 1.5E-18
2 g11395.t7 PANTHER PTHR10574 NETRIN/LAMININ-RELATED 51 132 7.7E-24
3 g11395.t7 PANTHER PTHR10574:SF197 LAMININ, BETA 2-LIKE 51 132 7.7E-24
1 g11395.t7 Pfam PF00055 Laminin N-terminal (Domain VI) 65 128 2.2E-13
9 g11395.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 26 -
10 g11395.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 10 -
11 g11395.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 11 21 -
12 g11395.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 22 26 -
8 g11395.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 135 -
7 g11395.t7 ProSiteProfiles PS51117 Laminin N-terminal domain profile. 61 135 11.47
5 g11395.t7 SignalP_EUK SignalP-TM SignalP-TM 1 26 -
4 g11395.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 10 29 -

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