General information for g7037.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Collagen alpha-1(II) chain.
Parent gene
- The parent gene g7037 is located on chr_2: 20761106..20766730 (- 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 | g7037 | g7037.t1 | TTS | g7037.t1 | 20761061 | 20761061 |
| chr_2 | g7037 | g7037.t1 | isoform | g7037.t1 | 20761106 | 20766730 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon1 | 20761106 | 20761916 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS1 | 20761106 | 20761916 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon2 | 20761979 | 20761987 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS2 | 20761979 | 20761987 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon3 | 20762044 | 20762098 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS3 | 20762044 | 20762098 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon4 | 20762158 | 20762185 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS4 | 20762158 | 20762185 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon5 | 20762241 | 20762285 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS5 | 20762241 | 20762285 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon6 | 20762346 | 20762417 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS6 | 20762346 | 20762417 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon7 | 20762474 | 20762535 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS7 | 20762474 | 20762535 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon8 | 20762606 | 20762633 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS8 | 20762606 | 20762633 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon9 | 20762697 | 20762731 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS9 | 20762697 | 20762731 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon10 | 20762796 | 20762813 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS10 | 20762796 | 20762813 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon11 | 20762883 | 20762928 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS11 | 20762883 | 20762928 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon12 | 20762985 | 20762992 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS12 | 20762985 | 20762992 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon13 | 20763056 | 20763073 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS13 | 20763056 | 20763073 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon14 | 20763142 | 20763168 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS14 | 20763142 | 20763168 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon15 | 20763234 | 20763278 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS15 | 20763234 | 20763278 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon16 | 20763452 | 20763479 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS16 | 20763452 | 20763479 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon17 | 20763703 | 20763791 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS17 | 20763703 | 20763791 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon18 | 20763928 | 20763963 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS18 | 20763928 | 20763963 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon19 | 20764032 | 20764058 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS19 | 20764032 | 20764058 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon20 | 20764117 | 20764134 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS20 | 20764117 | 20764134 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon21 | 20764218 | 20764245 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS21 | 20764218 | 20764245 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon22 | 20764410 | 20764476 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS22 | 20764410 | 20764476 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon23 | 20764532 | 20764571 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS23 | 20764532 | 20764571 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon24 | 20764641 | 20764659 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS24 | 20764641 | 20764659 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon25 | 20764722 | 20764739 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS25 | 20764722 | 20764739 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon26 | 20765269 | 20765302 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS26 | 20765269 | 20765302 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon27 | 20765374 | 20765447 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS27 | 20765374 | 20765447 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon28 | 20765522 | 20765565 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS28 | 20765522 | 20765565 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon29 | 20765691 | 20765754 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS29 | 20765691 | 20765754 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon30 | 20765821 | 20765838 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS30 | 20765821 | 20765838 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon31 | 20765901 | 20765917 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS31 | 20765901 | 20765917 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon32 | 20766139 | 20766179 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS32 | 20766139 | 20766179 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon33 | 20766246 | 20766258 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS33 | 20766246 | 20766258 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon34 | 20766321 | 20766340 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS34 | 20766321 | 20766340 |
| chr_2 | g7037 | g7037.t1 | exon | g7037.t1.exon35 | 20766726 | 20766730 |
| chr_2 | g7037 | g7037.t1 | cds | g7037.t1.CDS35 | 20766726 | 20766730 |
| chr_2 | g7037 | g7037.t1 | TSS | g7037.t1 | NA | NA |
Sequences
>g7037.t1 Gene=g7037 Length=2007
ATGATAGGAGAACCTGGAGAAAAAGGACCACCTGGAGAACCTGGAGCAGTTGGATCTGTT
GGGCCTGTTGGATTGCCTGGTCCTCAGGGCTTACAAGGATTTCCTGGACAACCTGGACCA
ATGGGATTGCCTGGTGTAAAAGGCGAACGCGGACTTATGGGAATTAAAGGAGAACAAGGT
AGTCAAGGTGAAAAAGGAATTACTGGTGAAGTTGGTCCTCCTGGTCCTATTGGATTAACT
GGCCAAAAAGGTGCCAGAGGAGATATTGGAGCAAGAGGAGAAGCTGGAATTATGGGTCCA
CCAGGACGACCAGGCGAAAATGGTGCTCCAGGTCAACCTGGGCAGCCTGGAATTCAAGGA
TTGCCAGGATTGCCGGGAATAAAAGGTGCTGTTGGAGAACAAGGAAGAATTGGAAATCCT
GGTCCAATGGGAAATCAAGGCCCACCCGGAACGCCGGGTGAAAAAGGAGACCCAGGAAGT
GATGGATCTCCAGGGCCGCAAGGAAATCAAGGGCCACAAGGACCTGCTGGAGATAGAGGA
ATGCCAGGTTTGCCGGGACCTGTCGGAGCTATGGGAGCAAAAGGAGCTAGAGGTGCACAA
GGAGAAAAGGGAGAAGCTGGAAAAGATGGAAAAGAAGGTCAACAAGGAGAAAGAGGAGCC
CAAGGAGAGCCTGGCCCAGTTGGCATGCCAGGTCCAGCAGGTGTTCCTGGTATTCAAGGA
CGAGTTGGTGATAAAGGACCAGTGGGAGCTCCTGGAAACACTGGACCCCCAGGTCCTCCG
GGATTGCCAGGTCCAACGGGACCAATCGGACCTGCAGGTGCTGCTGGAGAAAGAGGAACG
AAGGGTGAACAAGGTCAACAAGGGGTTGATGGTCCAATCGGTCCAAGAGGAAAACCAGGT
CCACCTGGAATTGAAGGAATAAAAGGTGAACGTGGAGAAGCAGGCGCCAAAGGAGCAAAA
GGTCACAGAGGATTAGTTGGTTTGCAGGGAATGACTGGAGCACCTGGATTAATTGGAGAA
AAAGGAAATCAAGGAAATATTGGACCTCAAGGACCACCTGGAGAAATGGGTCCTCGAGGT
CCTGCTGGAAGAGATGGAAGCCCAGGTCCACAAGGGTTACCAGGAAATATAGGCCCTAGA
GGTCCACAAGGAGAACCCGGAAAACCAGGATTAAGAGGTGATGTTGGTCCTCCAGGACCA
CCTGGACCACAAGCTGAATCAATTGGTTATGATGCAGCAGCATTAGCAGCTCTTTTAGGT
CATGGTGCGAATAATCAAAAGGGGCCAGATCCTAATGATGATCCTCTCAAACAATTATCA
GATGAAGAAAAACGTGCTATTGTTTTAAAGGCATATGAAAATCTCAAAGTTCGCTTTGAA
AAGTTCAAAAAACCAAATGGAGAGAAACTTTATCCTGCAAAAACTTGTCGTGATTTGGCA
GTTGCTTATCCTGAATATGAAAGCGGAAATTACTGGATTGATCCAAATGATGGTGATGCA
CGCGATGCTATTTTAGTATACTGTGATCTCAAAAAACGTGCAACATGTGTTATACCATCG
CCACTGAAATCTGATGAAATCAGTTATACTGGAAAAGAACCTGAAATTTGGTTGAGTGAG
CTTGAAAAGGGAATGAAGATCAATTATAAAGCAGATAGCAATCAAATGGGATTCTTGCAA
TTACTTTCAACACATGCCACTCAAAATATCACTTTCCATTGTAAAAATACTGTTGCATTC
TTTGATCGTCAAAAGAATAATCATCGAAAAGGTTTGAAACTCATGACTTGGAATGATAAT
GAATTGACACCAAAAGGACCACAAAGATTACGGTATGATGTCTCGGAAGACGGATGTCAA
GAGCGAACTAATTCATGGTCACAAACTGTCATTAGTTATACAACTGAAAAGCCTTTGAGA
CTTCCACTCATGGACATTGCTGTTCGTGATTTTGGTGAATCTGATCAAAAGTTTTGGATT
GAAATTAGTCCTGTTTGCTTCTATTAA
>g7037.t1 Gene=g7037 Length=668
MIGEPGEKGPPGEPGAVGSVGPVGLPGPQGLQGFPGQPGPMGLPGVKGERGLMGIKGEQG
SQGEKGITGEVGPPGPIGLTGQKGARGDIGARGEAGIMGPPGRPGENGAPGQPGQPGIQG
LPGLPGIKGAVGEQGRIGNPGPMGNQGPPGTPGEKGDPGSDGSPGPQGNQGPQGPAGDRG
MPGLPGPVGAMGAKGARGAQGEKGEAGKDGKEGQQGERGAQGEPGPVGMPGPAGVPGIQG
RVGDKGPVGAPGNTGPPGPPGLPGPTGPIGPAGAAGERGTKGEQGQQGVDGPIGPRGKPG
PPGIEGIKGERGEAGAKGAKGHRGLVGLQGMTGAPGLIGEKGNQGNIGPQGPPGEMGPRG
PAGRDGSPGPQGLPGNIGPRGPQGEPGKPGLRGDVGPPGPPGPQAESIGYDAAALAALLG
HGANNQKGPDPNDDPLKQLSDEEKRAIVLKAYENLKVRFEKFKKPNGEKLYPAKTCRDLA
VAYPEYESGNYWIDPNDGDARDAILVYCDLKKRATCVIPSPLKSDEISYTGKEPEIWLSE
LEKGMKINYKADSNQMGFLQLLSTHATQNITFHCKNTVAFFDRQKNNHRKGLKLMTWNDN
ELTPKGPQRLRYDVSEDGCQERTNSWSQTVISYTTEKPLRLPLMDIAVRDFGESDQKFWI
EISPVCFY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g7037.t1 | Gene3D | G3DSA:2.60.120.1000 | - | 450 | 668 | 1.1E-73 |
| 15 | g7037.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 36 | - |
| 17 | g7037.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 56 | 113 | - |
| 13 | g7037.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 131 | 306 | - |
| 16 | g7037.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 201 | 216 | - |
| 14 | g7037.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 252 | 267 | - |
| 8 | g7037.t1 | PANTHER | PTHR24023:SF569 | COLLAGEN ALPHA-1(I) CHAIN | 2 | 201 | 2.8E-127 |
| 11 | g7037.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 2 | 201 | 2.8E-127 |
| 7 | g7037.t1 | PANTHER | PTHR24023:SF569 | COLLAGEN ALPHA-1(I) CHAIN | 129 | 354 | 2.8E-127 |
| 10 | g7037.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 129 | 354 | 2.8E-127 |
| 6 | g7037.t1 | PANTHER | PTHR24023:SF569 | COLLAGEN ALPHA-1(I) CHAIN | 349 | 662 | 2.8E-127 |
| 9 | g7037.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 349 | 662 | 2.8E-127 |
| 3 | g7037.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 3 | 58 | 9.4E-10 |
| 1 | g7037.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 255 | 312 | 1.0E-6 |
| 2 | g7037.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 291 | 349 | 2.0E-9 |
| 4 | g7037.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 348 | 404 | 5.8E-9 |
| 5 | g7037.t1 | Pfam | PF01410 | Fibrillar collagen C-terminal domain | 448 | 667 | 4.4E-72 |
| 19 | g7037.t1 | ProSiteProfiles | PS51461 | Fibrillar collagen C-terminal non-collagenous (NC1) domain profile. | 442 | 668 | 74.484 |
| 12 | g7037.t1 | SMART | SM00038 | COLFI_2 | 445 | 668 | 1.7E-76 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005201 | extracellular matrix structural constituent | MF |
KEGG
Orthology
- This transcript has been annotated with K06236 (collagen type I 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.
