General information for g5873.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Laminin subunit alpha-1.
Parent gene
- The parent gene g5873 is located on chr_2: 12531093..12532805 (- 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_2 | g5873 | g5873.t4 | isoform | g5873.t4 | 12523818 | 12525550 |
| chr_2 | g5873 | g5873.t4 | exon | g5873.t4.exon1 | 12523818 | 12524073 |
| chr_2 | g5873 | g5873.t4 | cds | g5873.t4.CDS1 | 12523818 | 12524073 |
| chr_2 | g5873 | g5873.t4 | exon | g5873.t4.exon2 | 12524129 | 12525197 |
| chr_2 | g5873 | g5873.t4 | cds | g5873.t4.CDS2 | 12524129 | 12524685 |
| chr_2 | g5873 | g5873.t4 | exon | g5873.t4.exon3 | 12525260 | 12525550 |
| chr_2 | g5873 | g5873.t4 | TSS | g5873.t4 | NA | NA |
| chr_2 | g5873 | g5873.t4 | TTS | g5873.t4 | NA | NA |
Sequences
>g5873.t4 Gene=g5873 Length=1616
GTTGTAATTGTCATGTCAGTGGATCTGAGGATCGAGTTTGTAATTCCAAAACTGGTCAAT
GTAAGTGTCGTCCGCATGTCATCGGTCGAACGTGCGATCGCTGTGAACGTGGCTATTGGA
ATATCGATTCAAAGCAGGGATGCGAAAAGTGCGCGTGTAATCTCGATGGAAGCGAGCACG
AAAATTGTGACATCTATACAGGTGAATGTGCTTGTCGACAAGGCGTCGAAGGAATCAAAT
GCGATCGCTGTAAAAGTGGCTATTACGGCTTTTCATCAACTGGCTGTAAAAAGTGTAATG
TTTGTGACAGCCCGTCAAAAATTTGCGATCAAGAGACTGGGCGGTGTATTTGTCCACCTT
TAAGTCATGGTAATGATTGCCAGCATTGCTATCCAAATACATGGGGTTGGGAGAATTTAC
GAGGTTGCAAAAATTGTGATTGTAATCAATCTGGATCATTGAAACAATCTTGTGAAGTGC
TAACAGGTCAATGTGAATGTAAAGAAGGCTATGCAGGTAGAGCTTGCGATTATTGTGCTC
CTGGATATTATGGCTTTCCCAATTGTCAAAAATGTAATTGTGACATTCGAGGATCAAAAA
GTTATGATGATGAAATTATTGAATGTGATGAAAAAGGTCAATGCCCATGCAAGGAACTTG
TCACAGGTTTAAAATGCGATGAATGTCGTCAATCAACATTTGGATTGTCACAATACAACC
CACATGGTTGCACGAGATGTTTTTGTTTTGGTCGTTCACAAACTTGCGAGCAGAATGATT
TAATTTGGGCACAAGTGAGATTGATGGGGCCAAGAAATATTTCAGTCAATTATATCACTG
ATTATCACACTCCTTATTATCATGAAGATATTGAATATATAATTTTGACACATTCAAAAA
ATAATCATGTTTATCGTGAGACAGCACGCTATGACACTCGTAATGGATTAATGATAATGC
CTGGTCATTCTGGTGATATTATAATTGGCACAAGACGAGCATTTCACAGTCCAATTTATA
TAGATTTACCAAAAGAATTTCGAGGCGATAAAACGAGCAGTTATGGAGGCTTTTTAAATT
TTACTCTTAGCACATTTGAATATCGTACAAATTATCATTATGAACATTTAAATTCATTTC
CACTTGTGCAGCTTCACACTCATTATCATTTAACACTCAATTATTATCATAACGAGTACA
ATAATGATGTTGATTCATTCAGTGTTATTCTTCATGAATCTTATTGGAGACACGCATCTA
ATGGATATAATATAAGTCGTGCCATAATGATGACTGCATTGCAAAATATTAAACATATTT
TTCTTAGAGTCACAACATCACAAGATTTTGTTAGTCTCACTGTTGAAAATGCAACAATGT
CAATTGGAATGCCTCGTAATGGGAATAATAATGCAGCAATTGCTTCAGGAATTGAAAAGT
GTGATTGTCCAGAGTTATATTCTGGTGATTCATGTCAAGATCCAGCTGAAGGTTATTATC
GTTGGCGAAACACAACCACACCAACAAATTTATTAGAAGATCTCGTTGGAAAAGTCATCC
CATGTGAATGCAATGAAAGAAGTGACAAATGTGACAAAGAAACTGGTGAATGCATT
>g5873.t4 Gene=g5873 Length=271
MGPRNISVNYITDYHTPYYHEDIEYIILTHSKNNHVYRETARYDTRNGLMIMPGHSGDII
IGTRRAFHSPIYIDLPKEFRGDKTSSYGGFLNFTLSTFEYRTNYHYEHLNSFPLVQLHTH
YHLTLNYYHNEYNNDVDSFSVILHESYWRHASNGYNISRAIMMTALQNIKHIFLRVTTSQ
DFVSLTVENATMSIGMPRNGNNNAAIASGIEKCDCPELYSGDSCQDPAEGYYRWRNTTTP
TNLLEDLVGKVIPCECNERSDKCDKETGECI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5873.t4 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 36 | 193 | 0.0000000 |
| 5 | g5873.t4 | PANTHER | PTHR10574:SF405 | WING BLISTER, ISOFORM B | 36 | 193 | 0.0000000 |
| 2 | g5873.t4 | PANTHER | PTHR10574 | NETRIN/LAMININ-RELATED | 204 | 270 | 0.0000000 |
| 4 | g5873.t4 | PANTHER | PTHR10574:SF405 | WING BLISTER, ISOFORM B | 204 | 270 | 0.0000000 |
| 1 | g5873.t4 | Pfam | PF00052 | Laminin B (Domain IV) | 72 | 202 | 0.0000000 |
| 7 | g5873.t4 | ProSiteProfiles | PS51115 | Laminin IV type A domain profile. | 21 | 212 | 19.2290000 |
| 6 | g5873.t4 | SMART | SM00281 | LamB_3a | 67 | 197 | 0.0000001 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5873/g5873.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5873.t4.fa.iupred3.txt does not exist
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.
