General information for g5016.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Collagen alpha-2(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.t1 | isoform | g5016.t1 | 6470957 | 6473936 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon1 | 6470957 | 6470973 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS1 | 6470957 | 6470973 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon2 | 6471181 | 6471249 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS2 | 6471181 | 6471249 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon3 | 6471603 | 6471646 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS3 | 6471603 | 6471646 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon4 | 6472206 | 6472258 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS4 | 6472206 | 6472258 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon5 | 6472349 | 6472394 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS5 | 6472349 | 6472394 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon6 | 6472467 | 6472493 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS6 | 6472467 | 6472493 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon7 | 6472561 | 6472615 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS7 | 6472561 | 6472615 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon8 | 6472677 | 6472747 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS8 | 6472677 | 6472747 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon9 | 6472808 | 6472834 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS9 | 6472808 | 6472834 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon10 | 6472892 | 6472972 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS10 | 6472892 | 6472972 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon11 | 6473037 | 6473090 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS11 | 6473037 | 6473090 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon12 | 6473154 | 6473623 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS12 | 6473154 | 6473623 |
| chr_2 | g5016 | g5016.t1 | exon | g5016.t1.exon13 | 6473682 | 6473936 |
| chr_2 | g5016 | g5016.t1 | cds | g5016.t1.CDS13 | 6473682 | 6473936 |
| chr_2 | g5016 | g5016.t1 | TSS | g5016.t1 | NA | NA |
| chr_2 | g5016 | g5016.t1 | TTS | g5016.t1 | NA | NA |
Sequences
>g5016.t1 Gene=g5016 Length=1269
ATGAGAGCTGCTTATCGAGATGGAGTTCCTGGAATTGAAGGAAGAAAAGGTGAAAGAGGA
TTTCCGGGAGCTAAAGGCGAACAAGGTTTACCTGGACCCATTGGATTGCAAGGCGAAAAG
GGAGATATTGGTTTCCCTGGAAAGAATGGAATTAATGGTATTCCAGGTATAAAAGGAAAT
AAGGGAGAGCAAGGACCTCCAGGATTTGATGGTCCGCCTGGATTACCTGGCGACAAAGGA
TTCCCCGGTCCCAGAGGTCCTGAGGGAAAACCTGGACTGCAGGGATTACAAGGTGAAAAA
GGAGAACCAGGACTTCAAGCACCTCCACCCATTGTTGGAAAGCCTGGTTTGCCTGGCCCT
CAAGGACAAAAAGGAGATAGAGGTCCACCAGGTGAACCTGGATTGATTGGTTTGCAGGGT
GAAAGAGGAGAACAGGGAGAAATCGGTTTAATTGGTATTGAAGGACAAAGAGGCCCTCCA
GGACCGAGAGGTGAAATTGGTTTAGCAGGACCTCCCGGACGAGATGGAGCTCCGGGATTA
CCAGGTTTAAAAGGAAACCCAGGAGCACCATGTTCACCAGCACAAGATTATCTAACTGGT
CTTCTTTTGGTTAAACACAGTCAATCGGAAGAAATTCCACAATGCGATCCTGGACATGTT
AAATTATGGGAAGGATATTCATTGATGTATGTTGATGGCAATGATTATCCAGCAAATCAA
GATTTAGGCTCACCTGGTTCATGTGTTCGTAAATTCTCAACTATGCCAGTCATGGCATGT
GGACAGAATAATGTTTGCAACTATGCTTCACGTAATGATCGTACATTCTGGTTGTCAACA
TCTAAAGAAATTCCAATGATGCCTGTTTCTGAATTTGAAATGCGTCCATATATTTCACGT
TGTACTGTATGTGAAGTGCCATCAAATGTCATTGCTGTTCACAGTCAATCATTACAAGTT
CCAGAATGTCCATATGGATGGGATTCACTTTGGATTGGTTATACTTTCATGATGCATACT
GCCGTTGGACATGGCGGTGGTGGACAAGCTTTAGCTAGTCCTGGATCATGTTTGCAAGAT
TTCCGTGCAACACCATTTATCGAATGTAATGGAGGCAAAGGTCAATGTCATTATTATGAA
ACAATGACTAGTTTCTGGATGGTTACAATTGATCAACAAAATCAATTTAGAACACCAGAA
CAACAAACATTAAAGGCAGGATCACTACATACGAAAGTCTCAAGATGTAATGTTTGTATA
AGAATATAA
>g5016.t1 Gene=g5016 Length=422
MRAAYRDGVPGIEGRKGERGFPGAKGEQGLPGPIGLQGEKGDIGFPGKNGINGIPGIKGN
KGEQGPPGFDGPPGLPGDKGFPGPRGPEGKPGLQGLQGEKGEPGLQAPPPIVGKPGLPGP
QGQKGDRGPPGEPGLIGLQGERGEQGEIGLIGIEGQRGPPGPRGEIGLAGPPGRDGAPGL
PGLKGNPGAPCSPAQDYLTGLLLVKHSQSEEIPQCDPGHVKLWEGYSLMYVDGNDYPANQ
DLGSPGSCVRKFSTMPVMACGQNNVCNYASRNDRTFWLSTSKEIPMMPVSEFEMRPYISR
CTVCEVPSNVIAVHSQSLQVPECPYGWDSLWIGYTFMMHTAVGHGGGGQALASPGSCLQD
FRATPFIECNGGKGQCHYYETMTSFWMVTIDQQNQFRTPEQQTLKAGSLHTKVSRCNVCI
RI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g5016.t1 | Gene3D | G3DSA:2.170.240.10 | Noncollagenous (NC1) domain of collagen IV | 197 | 422 | 6.5E-107 |
| 12 | g5016.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 6 | g5016.t1 | PANTHER | PTHR24023:SF588 | COLLAGEN ALPHA-2(IV) CHAIN | 8 | 406 | 1.7E-140 |
| 7 | g5016.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 8 | 406 | 1.7E-140 |
| 5 | g5016.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 8 | 65 | 7.3E-10 |
| 3 | g5016.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 47 | 104 | 4.3E-10 |
| 4 | g5016.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 135 | 191 | 3.6E-10 |
| 2 | g5016.t1 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 202 | 305 | 2.9E-35 |
| 1 | g5016.t1 | Pfam | PF01413 | C-terminal tandem repeated domain in type 4 procollagen | 310 | 420 | 1.2E-39 |
| 14 | g5016.t1 | ProSiteProfiles | PS51403 | Collagen IV carboxyl-terminal non-collagenous (NC1) domain profile. | 200 | 422 | 113.186 |
| 11 | g5016.t1 | SMART | SM00111 | C4_2 | 200 | 307 | 1.9E-59 |
| 10 | g5016.t1 | SMART | SM00111 | C4_2 | 308 | 422 | 1.5E-67 |
| 8 | g5016.t1 | SUPERFAMILY | SSF56436 | C-type lectin-like | 202 | 309 | 9.18E-42 |
| 9 | g5016.t1 | SUPERFAMILY | SSF56436 | C-type lectin-like | 309 | 420 | 1.48E-42 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5016/g5016.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5016.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 transcript has been annotated with K06237 (collagen type IV alpha)
Pathway
- This transcript belongs to the following pathways
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.
