General information for g5016.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Collagen alpha-1(IV) chain.
Parent gene
- The parent gene g5016 is located on chr_2: 6473936..6474604 (+ 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 | g5016 | g5016.t7 | isoform | g5016.t7 | 6473090 | 6474604 |
| chr_2 | g5016 | g5016.t7 | exon | g5016.t7.exon1 | 6473090 | 6473623 |
| chr_2 | g5016 | g5016.t7 | cds | g5016.t7.CDS1 | 6473294 | 6473623 |
| chr_2 | g5016 | g5016.t7 | exon | g5016.t7.exon2 | 6473682 | 6474604 |
| chr_2 | g5016 | g5016.t7 | cds | g5016.t7.CDS2 | 6473682 | 6473936 |
| chr_2 | g5016 | g5016.t7 | TSS | g5016.t7 | NA | NA |
| chr_2 | g5016 | g5016.t7 | TTS | g5016.t7 | NA | NA |
Sequences
>g5016.t7 Gene=g5016 Length=1457
GGTATAAAATTCAAATTAATTAAATAATAGTTTTTTATTATAAATTTTTACTTTTTTTCA
ATAGGTTTAAAAGGAAACCCAGGAGCACCATGTTCACCAGCACAAGATTATCTAACTGGT
CTTCTTTTGGTTAAACACAGTCAATCGGAAGAAATTCCACAATGCGATCCTGGACATGTT
AAATTATGGGAAGGATATTCATTGATGTATGTTGATGGCAATGATTATCCAGCAAATCAA
GATTTAGGCTCACCTGGTTCATGTGTTCGTAAATTCTCAACTATGCCAGTCATGGCATGT
GGACAGAATAATGTTTGCAACTATGCTTCACGTAATGATCGTACATTCTGGTTGTCAACA
TCTAAAGAAATTCCAATGATGCCTGTTTCTGAATTTGAAATGCGTCCATATATTTCACGT
TGTACTGTATGTGAAGTGCCATCAAATGTCATTGCTGTTCACAGTCAATCATTACAAGTT
CCAGAATGTCCATATGGATGGGATTCACTTTGGATTGGTTATACTTTCATGATGCATACT
GCCGTTGGACATGGCGGTGGTGGACAAGCTTTAGCTAGTCCTGGATCATGTTTGCAAGAT
TTCCGTGCAACACCATTTATCGAATGTAATGGAGGCAAAGGTCAATGTCATTATTATGAA
ACAATGACTAGTTTCTGGATGGTTACAATTGATCAACAAAATCAATTTAGAACACCAGAA
CAACAAACATTAAAGGCAGGATCACTACATACGAAAGTCTCAAGATGTAATGTTTGTATA
AGAATATAATGATACATATATATTATTTAAGAATACAGAAAAATTCCTTCCCGATATTGT
TCTTTTCTTTTACTCTTTCATAAATGTGTGCCAAAAAGTAGAATTTTATGTTTCACATCT
CTTTTCATTTTTTCTTTGCAAAATATCATCTTATCAAATATTGTGAAAGAGTGCGAGATA
TTTCTTTTTATTCTTACTAACTGTAAAAAATCAATATAGAAAGAATGCCAAAGTAGCAGA
GCAGACAAGAATGTGAGATAAAGAAGAAAAAGAAATTGATTCTTTTTAAAAAAAATTATT
TTTTTCATCGATTTAATTTGTTTGTTTTTCATGCCATATGTTACCAAAAGAGTAAACAAA
TCAACACTAAAATCATTATATAAATTTTTTAGATAATGGCAAATTAATTTTAAAAATTAA
AAATTTTCTTAAATTTTAACAAGTCTTAGACTTTTTTAAATTGAATATGATCAATGATCT
GCCAAAATACTGCCTCTTTATATTGCATAAAAATAATAATTATTAATAATAATGATAATA
ATACCTACCTAGTAATGATTTAACGAAAAAACATAAATTTATAATTTACTACAATCTTCT
GTCTTAATTTGATAATTCATAATGTAATAAAAACTTCAATTTTCAAGATATTCAAAAAAA
AAATCTTTTATTTTATT
>g5016.t7 Gene=g5016 Length=194
MYVDGNDYPANQDLGSPGSCVRKFSTMPVMACGQNNVCNYASRNDRTFWLSTSKEIPMMP
VSEFEMRPYISRCTVCEVPSNVIAVHSQSLQVPECPYGWDSLWIGYTFMMHTAVGHGGGG
QALASPGSCLQDFRATPFIECNGGKGQCHYYETMTSFWMVTIDQQNQFRTPEQQTLKAGS
LHTKVSRCNVCIRI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5016.t7 | Gene3D | G3DSA:2.170.240.10 | Noncollagenous (NC1) domain of collagen IV | 1 | 194 | 0.000 |
| 3 | g5016.t7 | PANTHER | PTHR24023:SF588 | COLLAGEN ALPHA-2(IV) CHAIN | 1 | 179 | 0.000 |
| 4 | g5016.t7 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 1 | 179 | 0.000 |
| 2 | g5016.t7 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 2 | 77 | 0.000 |
| 1 | g5016.t7 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 82 | 192 | 0.000 |
| 10 | g5016.t7 | ProSiteProfiles | PS51403 | Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. | 1 | 194 | 98.766 |
| 8 | g5016.t7 | SMART | SM00111 | C4_2 | 1 | 79 | 0.000 |
| 7 | g5016.t7 | SMART | SM00111 | C4_2 | 80 | 194 | 0.000 |
| 6 | g5016.t7 | SUPERFAMILY | SSF56436 | C-type lectin-like | 2 | 81 | 0.000 |
| 5 | g5016.t7 | SUPERFAMILY | SSF56436 | C-type lectin-like | 81 | 192 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5016/g5016.t7; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5016.t7.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.
