General information for g12075.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cryptochrome-1.
Parent gene
- The parent gene g12075 is located on chr_1: 20812382..20813354 (- 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_1 | g12075 | g12075.t9 | isoform | g12075.t9 | 20812382 | 20813354 |
| chr_1 | g12075 | g12075.t9 | exon | g12075.t9.exon1 | 20812382 | 20812392 |
| chr_1 | g12075 | g12075.t9 | cds | g12075.t9.CDS1 | 20812384 | 20812392 |
| chr_1 | g12075 | g12075.t9 | exon | g12075.t9.exon2 | 20812453 | 20812601 |
| chr_1 | g12075 | g12075.t9 | cds | g12075.t9.CDS2 | 20812453 | 20812601 |
| chr_1 | g12075 | g12075.t9 | exon | g12075.t9.exon3 | 20812661 | 20812966 |
| chr_1 | g12075 | g12075.t9 | cds | g12075.t9.CDS3 | 20812661 | 20812966 |
| chr_1 | g12075 | g12075.t9 | exon | g12075.t9.exon4 | 20813150 | 20813247 |
| chr_1 | g12075 | g12075.t9 | cds | g12075.t9.CDS4 | 20813150 | 20813247 |
| chr_1 | g12075 | g12075.t9 | exon | g12075.t9.exon5 | 20813314 | 20813354 |
| chr_1 | g12075 | g12075.t9 | cds | g12075.t9.CDS5 | 20813314 | 20813354 |
| chr_1 | g12075 | g12075.t9 | TSS | g12075.t9 | 20813433 | 20813433 |
| chr_1 | g12075 | g12075.t9 | TTS | g12075.t9 | NA | NA |
Sequences
>g12075.t9 Gene=g12075 Length=605
ATGGAAGTTAAATCAATTATTTGGTTTCGCCATGGCCTAAGAATTCACGATAATCCAGCC
CTATTAGAGGCGATAAAATCAGAAGGCTCATCGAAAGTGACATTTTATCCAGTGTTCATT
TTTGATGGAATAACCGCAGGAACGAAACTAGTTGGATACAATCGAATGAAATTTTTAATT
GAATCTCTAGAAGATTTAAATGAACAATTTAAAAGCTTTGGTGGAAATGGATTACATATT
TTTCGAGGTGACCCGGTAGAAATTTTTACTAAACTTTCAAAAGAACTTGGCATCAATAAA
ATATGTTTCGAGCAAGATTGCGAACCAATATGGAATGAAAGAGATATGAGAGTAGCTCAA
ATGTGTAAAGAACTTGATATTACATTGATTGAAAAAATTTCTCATACTTTATGGGATCCG
AATTCTGTAATCAATGCCAACGGGGGCTATCCTCCACTCACATATCAAATGTTTCTGCAC
ACTGTCAATGTATTAGGCAATCCTTCAAGACCTGTTCAAATGCCTTGCTTTTCTAATGTC
GTTTTTGGAACTATCCCACTTCATTTGCATAAACAACTTGGGTTGATGAACTCGATTCCA
TCACC
>g12075.t9 Gene=g12075 Length=201
MEVKSIIWFRHGLRIHDNPALLEAIKSEGSSKVTFYPVFIFDGITAGTKLVGYNRMKFLI
ESLEDLNEQFKSFGGNGLHIFRGDPVEIFTKLSKELGINKICFEQDCEPIWNERDMRVAQ
MCKELDITLIEKISHTLWDPNSVINANGGYPPLTYQMFLHTVNVLGNPSRPVQMPCFSNV
VFGTIPLHLHKQLGLMNSIPS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g12075.t9 | Gene3D | G3DSA:3.40.50.620 | HUPs | 2 | 134 | 0.0000000 |
| 6 | g12075.t9 | Gene3D | G3DSA:1.25.40.80 | - | 135 | 179 | 0.0000004 |
| 2 | g12075.t9 | PANTHER | PTHR11455 | CRYPTOCHROME | 4 | 201 | 0.0000000 |
| 3 | g12075.t9 | PANTHER | PTHR11455:SF17 | CRYPTOCHROME-1 | 4 | 201 | 0.0000000 |
| 1 | g12075.t9 | Pfam | PF00875 | DNA photolyase | 5 | 163 | 0.0000000 |
| 7 | g12075.t9 | ProSiteProfiles | PS51645 | Photolyase/cryptochrome alpha/beta domain profile. | 3 | 137 | 32.4110000 |
| 4 | g12075.t9 | SUPERFAMILY | SSF52425 | Cryptochrome/photolyase, N-terminal domain | 5 | 176 | 0.0000000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
