General information for g5014.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Collagen alpha-1(IV) chain.
Parent gene
- The parent gene g5014 is located on chr_2: 6467796..6470286 (+ 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 | g5014 | g5014.t1 | isoform | g5014.t1 | 6464759 | 6467865 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon1 | 6464759 | 6464798 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS1 | 6464759 | 6464798 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon2 | 6465140 | 6465194 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS2 | 6465140 | 6465194 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon3 | 6465258 | 6465283 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS3 | 6465258 | 6465283 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon4 | 6465345 | 6465493 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS4 | 6465345 | 6465493 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon5 | 6465607 | 6465655 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS5 | 6465607 | 6465655 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon6 | 6465772 | 6465808 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS6 | 6465772 | 6465808 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon7 | 6465892 | 6465968 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS7 | 6465892 | 6465968 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon8 | 6466130 | 6466159 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS8 | 6466130 | 6466159 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon9 | 6466220 | 6466261 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS9 | 6466220 | 6466261 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon10 | 6466334 | 6466405 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS10 | 6466334 | 6466405 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon11 | 6466512 | 6466563 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS11 | 6466512 | 6466563 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon12 | 6466720 | 6466772 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS12 | 6466720 | 6466772 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon13 | 6466900 | 6467000 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS13 | 6466900 | 6467000 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon14 | 6467088 | 6467114 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS14 | 6467088 | 6467114 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon15 | 6467175 | 6467238 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS15 | 6467175 | 6467238 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon16 | 6467294 | 6467370 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS16 | 6467294 | 6467370 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon17 | 6467523 | 6467550 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS17 | 6467523 | 6467550 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon18 | 6467614 | 6467649 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS18 | 6467614 | 6467649 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon19 | 6467710 | 6467740 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS19 | 6467710 | 6467740 |
| chr_2 | g5014 | g5014.t1 | exon | g5014.t1.exon20 | 6467796 | 6467865 |
| chr_2 | g5014 | g5014.t1 | cds | g5014.t1.CDS20 | 6467796 | 6467865 |
| chr_2 | g5014 | g5014.t1 | TSS | g5014.t1 | NA | NA |
| chr_2 | g5014 | g5014.t1 | TTS | g5014.t1 | NA | NA |
Sequences
>g5014.t1 Gene=g5014 Length=1116
ATGAGAAGATGCATATCTTCTGGTGGAAGATTCCATCCAAGAAAACAAGGTGAACGTGGA
GAAAAAGGTGAAAAAGGAGATATTGGATTTGAAGGTTTGCCTGGTATTGCTGGAGCGCCA
GGTCCTATGGGTCCAAAAGGAGATATTGGATTAATTGGACCAGCTGGTTTACCGGGTCTC
GACGGACAAAAAGGCGATCAAGGATTTATGGGACCAACAGGACCTAAAGGAGAGCCTGGC
GATGTTTCAGAAAAGGGACAAAAAGGAGAGGTCGGTCCACCAGGATTGAGAGGAATTGAT
GGTAGACCAGGCTTAGATGGCTTGCCTGGGCCAAAAGGTGATGCTGGACTTCCTGGATAC
GGTCAACCTGGTCCACAAGGTGAAAGAGGAAAAGATGGATTAGATGGTCTTCCTGGTCTC
GATGGACAAAAAGGTGACATTGGTCTTCCTGGTTTTCCTGGAGTCAAGGGAGATAAAGGA
AATATGGGACCAAATGGAATTCCAGGATCACCTGGTCTTGATGGACTAAAAGGAAATGAA
GGTCCAATGGGAGCTCCTGGACCGATGGGACCAAAAGGCCAAAAGGGTGAACAAGGTTTG
CCGGGAATAGGTGAAAGAGGTGACACAGGTCTTCCGGGACCAATTGGTTATCCTGGAGTG
AAAGGTGAAAGAGGTCCACAAGGTGAAAGAGGTCTGCCAGGTCCGATTGCAGAAATTAAA
GGAGAAAAAGGTGACAGAGGTTTACCAGGTTTGATTGGATTGCAAGGAGAAATGGGACCA
CCAGGACCAAAAGGTGAACCAGGCCCAGCGGGACCAAGAGGTCTTCCTGGTATGGATGGA
ATTCAAGGACAAAAAGGAGAGCAAGGTTTAATTGGTGAAAGAGGAGATGTTGGTCCAACT
GTTAAAGGAGAAAAAGGCCTCCCAGGAAGACCTGGAAAGAATGGTCGTGATGGTTTAATT
GGTATGCCTGGCGAAAAAGGTGAAAGAGGGCTTCCAGGTCTCGATGGAGTACCAGGACCG
AGAGGCTTACCTGGTCCAGTTGGAAGACCTGGTGAAAAAGGAGACAGAGGTGCTCCAGGT
AAGTCATTAAATTTTTGTCTTAAAAAATGCAAATAA
>g5014.t1 Gene=g5014 Length=371
MRRCISSGGRFHPRKQGERGEKGEKGDIGFEGLPGIAGAPGPMGPKGDIGLIGPAGLPGL
DGQKGDQGFMGPTGPKGEPGDVSEKGQKGEVGPPGLRGIDGRPGLDGLPGPKGDAGLPGY
GQPGPQGERGKDGLDGLPGLDGQKGDIGLPGFPGVKGDKGNMGPNGIPGSPGLDGLKGNE
GPMGAPGPMGPKGQKGEQGLPGIGERGDTGLPGPIGYPGVKGERGPQGERGLPGPIAEIK
GEKGDRGLPGLIGLQGEMGPPGPKGEPGPAGPRGLPGMDGIQGQKGEQGLIGERGDVGPT
VKGEKGLPGRPGKNGRDGLIGMPGEKGERGLPGLDGVPGPRGLPGPVGRPGEKGDRGAPG
KSLNFCLKKCK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g5014.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 28 | - |
| 14 | g5014.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 12 | 28 | - |
| 13 | g5014.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 76 | 99 | - |
| 12 | g5014.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 290 | 371 | - |
| 8 | g5014.t1 | PANTHER | PTHR24023:SF897 | MACROPHAGE RECEPTOR MARCO | 15 | 202 | 9.3E-71 |
| 11 | g5014.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 15 | 202 | 9.3E-71 |
| 6 | g5014.t1 | PANTHER | PTHR24023:SF897 | MACROPHAGE RECEPTOR MARCO | 121 | 318 | 9.3E-71 |
| 9 | g5014.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 121 | 318 | 9.3E-71 |
| 7 | g5014.t1 | PANTHER | PTHR24023:SF897 | MACROPHAGE RECEPTOR MARCO | 204 | 361 | 9.3E-71 |
| 10 | g5014.t1 | PANTHER | PTHR24023 | COLLAGEN ALPHA | 204 | 361 | 9.3E-71 |
| 4 | g5014.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 15 | 72 | 9.6E-10 |
| 2 | g5014.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 62 | 118 | 6.7E-9 |
| 1 | g5014.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 121 | 175 | 2.3E-7 |
| 3 | g5014.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 259 | 299 | 8.5E-8 |
| 5 | g5014.t1 | Pfam | PF01391 | Collagen triple helix repeat (20 copies) | 303 | 361 | 2.4E-10 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5014/g5014.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5014.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K24355 (collagen type XXIII 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.
