General information for g5801.t38
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Collagen alpha-5(IV) chain.
Parent gene
- The parent gene g5801 is located on chr_2: 11988122..11991182 (- 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 | g5801 | g5801.t38 | isoform | g5801.t38 | 11988033 | 11989373 |
| chr_2 | g5801 | g5801.t38 | exon | g5801.t38.exon1 | 11988033 | 11989373 |
| chr_2 | g5801 | g5801.t38 | TTS | g5801.t38 | 11988062 | 11988062 |
| chr_2 | g5801 | g5801.t38 | cds | g5801.t38.CDS1 | 11988122 | 11988853 |
| chr_2 | g5801 | g5801.t38 | TSS | g5801.t38 | NA | NA |
Sequences
>g5801.t38 Gene=g5801 Length=1341
GGTAAAATTTTTATTTTAATATTCAGCTCACTAATACACTCTATTTTAAAATATATAAAT
GTTAAACTCATGTTTAATTATTTTTATAGGTTTAACTGGATTACCCGGTGCTCCAGGATT
AAAAGGTCAGAAATTGAATTATAATAACATTGAACGAGTTTTATTATTCATTTAAAATTT
TTACAATAGGAGAAAAAGGTTTCAGAGGACCGCCAGGTGTCAATGGACTAGGTAATTTTT
GTCATATCAGTTTATTTTACTTCTAATTTATTAAACGTCTTTTTTAGATGGATTTAGAGG
ACCACCAGGTGAAAATGGCGATGATGCACCACCACCTCCTCCACCAAAAAGTCGTGGCTT
TGTTTTCACTCGTCACTCACAATCAGTAACTGTGCCAAGATGTCCAGTCAATACAAATCT
TCTTTGGGAGGGATACTCATTCGTATCAATTATTGGAAGTGGTCGCTCTGTTGGGCAAGA
TTTGGGCACATCTGGGTCATGTTTAAGACAATTCTCAACAATGCCATTCATGTTCTGCAA
TTTGAACAATGTATGCAGCTATGCAGAAAACAATGACGACAGCATCTGGCTAACAACAGG
TGAACCAATGCCAATGTCAATGACTCCTATTCCAGCAAGAGAAATGGAGAAATATGTCTC
AAGATGTGCAGTATGTGAAACAACAACACGTCTTATTGCTCTTCACAGTCAAAGTATGGA
AATTCCTGATTGTCCTCAAGGATGGGAAGAAGCATGGATCGGTTACAGTTATTATATGCA
GACTTCTGATGCTAACGGCAACTCTCATCAAAATCTTATTTCACCTGGTTCATGTTTGGA
AGAATTTAGAGCTCAACCAGTTATTGAATGTCACGGTCGTGGTTCATGCAACATTTTTGA
TGGTATCACATCATTCTGGTTAACAGTTATTGAAGATAGTGAACAATTCCGAAAACCAAA
GCAACAAACATTGAAGGCTGATCAGACAAGCAAAATCAGTCGTTGCTCAGTATGTCGTAA
AATGGACAACAGCCTCAGAAGTCGTACAGTTAGTCGTGTGCAACTACCGAATGCTTCTGC
ATTCTCTCAAAGAGAAACGGAGATTTCAAATTCATTCAGAAGCAATGATGTTACGGCAAT
CAATCAGCCAGAAGTTCAACGCTTCCCTCAACCACCAAGAAGAAGACCAAGACCAGGCAG
TCGCACTAGTCCGAGACGTTCAAATCGCTCGAGAGATCAGCAGCAAGGCTAAATAATAGT
AAATAGTTTTTTTAAGATGCCATATGTCTTCAGTTGATGCAACTAACTAGCCAAAAATAA
AAAAATATTGAATAATAAAGT
>g5801.t38 Gene=g5801 Length=243
MPFMFCNLNNVCSYAENNDDSIWLTTGEPMPMSMTPIPAREMEKYVSRCAVCETTTRLIA
LHSQSMEIPDCPQGWEEAWIGYSYYMQTSDANGNSHQNLISPGSCLEEFRAQPVIECHGR
GSCNIFDGITSFWLTVIEDSEQFRKPKQQTLKADQTSKISRCSVCRKMDNSLRSRTVSRV
QLPNASAFSQRETEISNSFRSNDVTAINQPEVQRFPQPPRRRPRPGSRTSPRRSNRSRDQ
QQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g5801.t38 | Gene3D | G3DSA:2.170.240.10 | Noncollagenous (NC1) domain of collagen IV | 1 | 169 | 4.5E-74 |
| 9 | g5801.t38 | MobiDBLite | mobidb-lite | consensus disorder prediction | 186 | 243 | - |
| 10 | g5801.t38 | MobiDBLite | mobidb-lite | consensus disorder prediction | 186 | 212 | - |
| 3 | g5801.t38 | PANTHER | PTHR24023:SF980 | COLLAGEN ALPHA-3(IV) CHAIN | 1 | 156 | 3.1E-59 |
| 4 | g5801.t38 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 1 | 156 | 3.1E-59 |
| 2 | g5801.t38 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 1 | 53 | 6.5E-12 |
| 1 | g5801.t38 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 58 | 166 | 5.2E-37 |
| 12 | g5801.t38 | ProSiteProfiles | PS51403 | Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. | 1 | 169 | 77.562 |
| 8 | g5801.t38 | SMART | SM00111 | C4_2 | 1 | 55 | 7.3E-7 |
| 7 | g5801.t38 | SMART | SM00111 | C4_2 | 56 | 168 | 1.8E-59 |
| 5 | g5801.t38 | SUPERFAMILY | SSF56436 | C-type lectin-like | 1 | 54 | 1.86E-15 |
| 6 | g5801.t38 | SUPERFAMILY | SSF56436 | C-type lectin-like | 57 | 167 | 3.06E-39 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5801/g5801.t38; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5801.t38.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005201 | extracellular matrix structural constituent | MF |
| GO:0005581 | collagen trimer | CC |
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.
