General information for g5801.t1
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 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.t1 | TTS | g5801.t1 | 11988062 | 11988062 |
| chr_2 | g5801 | g5801.t1 | isoform | g5801.t1 | 11988122 | 11991182 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon1 | 11988122 | 11989086 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS1 | 11988122 | 11989086 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon2 | 11989143 | 11989184 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS2 | 11989143 | 11989184 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon3 | 11989249 | 11989284 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS3 | 11989249 | 11989284 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon4 | 11989373 | 11989407 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS4 | 11989373 | 11989407 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon5 | 11990129 | 11990156 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS5 | 11990129 | 11990156 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon6 | 11990220 | 11990238 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS6 | 11990220 | 11990238 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon7 | 11990308 | 11990408 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS7 | 11990308 | 11990408 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon8 | 11990477 | 11990539 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS8 | 11990477 | 11990539 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon9 | 11990623 | 11990685 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS9 | 11990623 | 11990685 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon10 | 11990752 | 11990820 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS10 | 11990752 | 11990820 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon11 | 11990919 | 11990963 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS11 | 11990919 | 11990963 |
| chr_2 | g5801 | g5801.t1 | exon | g5801.t1.exon12 | 11991104 | 11991182 |
| chr_2 | g5801 | g5801.t1 | cds | g5801.t1.CDS12 | 11991104 | 11991182 |
| chr_2 | g5801 | g5801.t1 | TSS | g5801.t1 | NA | NA |
Sequences
>g5801.t1 Gene=g5801 Length=1545
ATGATCTTTTTTTATAGTGCTGATGGTGTTAAAGGTATTGTTGGTGACATCGGCTTTCAA
GGACCAGTTGGCTTACCAGGCTTAGATGGACTGCCAGGATTAAGAGGAGATATTGGATTC
CCAGGACTACAAGGAGATATTGGGTATTCAATTCCTGGAATTAAGGGTGAACGTGGTGAT
GTTGGTTTACCAGGTTTCGATGGAATTGACGGTCTTGATGGAGAAGTTGGTGATATTGGT
GAAACAGGAGCGCCAGGATTTAGAGGTAGAAAAGGTGAAAGAGGACTAATTGGAGATATT
GGTGAAGAAGGATTCGAAGGTCGCGAAGGATTAATAGGACTTAAAGGCATGAAAGGTGAT
CCAGCACCTTTAAATCAATTCAGACCAAAACCAGGATATGATGGTTTAAGAGGAGAAAAG
GGTGAAACCGGTGACAAAGGCTTCCCAGGCACACCAGGATTAGTTGGTTATCGAGGTCTG
AAAGGTTATCAAGGATTACAAGGTTTAACTGGATTACCCGGTGCTCCAGGATTAAAAGGA
GAAAAAGGTTTCAGAGGACCGCCAGGTGTCAATGGACTAGATGGATTTAGAGGACCACCA
GGTGAAAATGGCGATGATGCACCACCACCTCCTCCACCAAAAAGTCGTGGCTTTGTTTTC
ACTCGTCACTCACAATCAGTAACTGTGCCAAGATGTCCAGTCAATACAAATCTTCTTTGG
GAGGGATACTCATTCGTATCAATTATTGGAAGTGGTCGCTCTGTTGGGCAAGATTTGGGC
ACATCTGGGTCATGTTTAAGACAATTCTCAACAATGCCATTCATGTTCTGCAATTTGAAC
AATGTATGCAGCTATGCAGAAAACAATGACGACAGCATCTGGCTAACAACAGGTGAACCA
ATGCCAATGTCAATGACTCCTATTCCAGCAAGAGAAATGGAGAAATATGTCTCAAGATGT
GCAGTATGTGAAACAACAACACGTCTTATTGCTCTTCACAGTCAAAGTATGGAAATTCCT
GATTGTCCTCAAGGATGGGAAGAAGCATGGATCGGTTACAGTTATTATATGCAGACTTCT
GATGCTAACGGCAACTCTCATCAAAATCTTATTTCACCTGGTTCATGTTTGGAAGAATTT
AGAGCTCAACCAGTTATTGAATGTCACGGTCGTGGTTCATGCAACATTTTTGATGGTATC
ACATCATTCTGGTTAACAGTTATTGAAGATAGTGAACAATTCCGAAAACCAAAGCAACAA
ACATTGAAGGCTGATCAGACAAGCAAAATCAGTCGTTGCTCAGTATGTCGTAAAATGGAC
AACAGCCTCAGAAGTCGTACAGTTAGTCGTGTGCAACTACCGAATGCTTCTGCATTCTCT
CAAAGAGAAACGGAGATTTCAAATTCATTCAGAAGCAATGATGTTACGGCAATCAATCAG
CCAGAAGTTCAACGCTTCCCTCAACCACCAAGAAGAAGACCAAGACCAGGCAGTCGCACT
AGTCCGAGACGTTCAAATCGCTCGAGAGATCAGCAGCAAGGCTAA
>g5801.t1 Gene=g5801 Length=514
MIFFYSADGVKGIVGDIGFQGPVGLPGLDGLPGLRGDIGFPGLQGDIGYSIPGIKGERGD
VGLPGFDGIDGLDGEVGDIGETGAPGFRGRKGERGLIGDIGEEGFEGREGLIGLKGMKGD
PAPLNQFRPKPGYDGLRGEKGETGDKGFPGTPGLVGYRGLKGYQGLQGLTGLPGAPGLKG
EKGFRGPPGVNGLDGFRGPPGENGDDAPPPPPPKSRGFVFTRHSQSVTVPRCPVNTNLLW
EGYSFVSIIGSGRSVGQDLGTSGSCLRQFSTMPFMFCNLNNVCSYAENNDDSIWLTTGEP
MPMSMTPIPAREMEKYVSRCAVCETTTRLIALHSQSMEIPDCPQGWEEAWIGYSYYMQTS
DANGNSHQNLISPGSCLEEFRAQPVIECHGRGSCNIFDGITSFWLTVIEDSEQFRKPKQQ
TLKADQTSKISRCSVCRKMDNSLRSRTVSRVQLPNASAFSQRETEISNSFRSNDVTAINQ
PEVQRFPQPPRRRPRPGSRTSPRRSNRSRDQQQG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g5801.t1 | Gene3D | G3DSA:2.170.240.10 | Noncollagenous (NC1) domain of collagen IV | 214 | 440 | 8.1E-102 |
| 12 | g5801.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 457 | 514 | - |
| 13 | g5801.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 457 | 483 | - |
| 5 | g5801.t1 | PANTHER | PTHR24023:SF980 | COLLAGEN ALPHA-3(IV) CHAIN | 8 | 46 | 2.2E-125 |
| 7 | g5801.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 8 | 46 | 2.2E-125 |
| 4 | g5801.t1 | PANTHER | PTHR24023:SF980 | COLLAGEN ALPHA-3(IV) CHAIN | 45 | 426 | 2.2E-125 |
| 6 | g5801.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 45 | 426 | 2.2E-125 |
| 3 | g5801.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 150 | 208 | 1.3E-10 |
| 2 | g5801.t1 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 219 | 324 | 3.7E-37 |
| 1 | g5801.t1 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 329 | 437 | 2.3E-36 |
| 15 | g5801.t1 | ProSiteProfiles | PS51403 | Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. | 217 | 440 | 102.742 |
| 10 | g5801.t1 | SMART | SM00111 | C4_2 | 217 | 326 | 5.1E-58 |
| 11 | g5801.t1 | SMART | SM00111 | C4_2 | 327 | 439 | 1.8E-59 |
| 8 | g5801.t1 | SUPERFAMILY | SSF56436 | C-type lectin-like | 215 | 325 | 4.47E-42 |
| 9 | g5801.t1 | SUPERFAMILY | SSF56436 | C-type lectin-like | 328 | 438 | 1.39E-38 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5801/g5801.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5801.t1.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.
