General information for g12075.t1
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.t1 | TTS | g12075.t1 | 20810964 | 20810964 |
| chr_1 | g12075 | g12075.t1 | isoform | g12075.t1 | 20811230 | 20813354 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon1 | 20811230 | 20811624 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS1 | 20811230 | 20811624 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon2 | 20811680 | 20811765 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS2 | 20811680 | 20811765 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon3 | 20811854 | 20812392 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS3 | 20811854 | 20812392 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon4 | 20812453 | 20812601 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS4 | 20812453 | 20812601 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon5 | 20812661 | 20812966 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS5 | 20812661 | 20812966 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon6 | 20813150 | 20813247 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS6 | 20813150 | 20813247 |
| chr_1 | g12075 | g12075.t1 | exon | g12075.t1.exon7 | 20813314 | 20813354 |
| chr_1 | g12075 | g12075.t1 | cds | g12075.t1.CDS7 | 20813314 | 20813354 |
| chr_1 | g12075 | g12075.t1 | TSS | g12075.t1 | 20813433 | 20813433 |
Sequences
>g12075.t1 Gene=g12075 Length=1614
ATGGAAGTTAAATCAATTATTTGGTTTCGCCATGGCCTAAGAATTCACGATAATCCAGCC
CTATTAGAGGCGATAAAATCAGAAGGCTCATCGAAAGTGACATTTTATCCAGTGTTCATT
TTTGATGGAATAACCGCAGGAACGAAACTAGTTGGATACAATCGAATGAAATTTTTAATT
GAATCTCTAGAAGATTTAAATGAACAATTTAAAAGCTTTGGTGGAAATGGATTACATATT
TTTCGAGGTGACCCGGTAGAAATTTTTACTAAACTTTCAAAAGAACTTGGCATCAATAAA
ATATGTTTCGAGCAAGATTGCGAACCAATATGGAATGAAAGAGATATGAGAGTAGCTCAA
ATGTGTAAAGAACTTGATATTACATTGATTGAAAAAATTTCTCATACTTTATGGGATCCG
AATTCTGTAATCAATGCCAACGGGGGCTATCCTCCACTCACATATCAAATGTTTCTGCAC
ACTGTCAATGTATTAGGCAATCCTTCAAGACCTGTTCAAATGCCTTGCTTTTCTAATGTC
GTTTTTGGAACTATCCCACTTCATTTGCATAAACAACTTGGGTTGATGAACTCGATTCCA
TCACCTGAAGATTTTTCGCTATTTCCTTCAAAATCTAAAAAATTCTTAGTCTGGAAAGGA
GGTGAAAAAAGAGCATTAGAGCAATTAAAAATTAGACTACAAGTTGAACAAGAAGCATTT
TTGAATGGAACTTATTTGCCTAATCAAGGCAATCCTAAATTAACAGGTGACTCTACATCA
ATGTCTGCTGCATTACGTTTTGGTTGCTTATCTGTGCGAAAGTTCTTTTATGATATTCAT
GATTTATTTGCTGAAGTAAAGCAAAAGACATTTAGTAATACTCCTGGCGGCCATCATATC
ACAGGACAATTGATTTGGCGAGAATATTTTTATACAATGAGTGTAAGAAATCCATTTTAT
GCACAAATGGAAAACAATCCCATTTGTTTGAATATTAATTGGTCGCGACCAAATGATGAA
GACATCTTGAAATGGAAGGAAGGTAGGACAGGTTTTCCAATTATAGACGCAAGCATGCGA
CAAATTCTATCAGAAGGTTGGATTCATCATACATTGCGAAATATTACAGCAACCTTCTTA
ACCCGTACAGGATTATGGTACAGTTGGGAGATTGGTTTACAGCATTTCTTAAAGTATCTT
CTCGATGCTGATTGGTCAGTGTGCAGCGGAAATTGGCTTTGGGTCTCATCAAGTGCATTT
GAACGCTTATTGGATTCATCAAAGTTTAGTATCATAGCTATTGCTTATCGTCTTGACCCG
GAAGGCACATATATTCGTCGATACATTCGTGAATTACGTGATATACCTAATAGATATATT
CATGAACCATGGAAAACACCATTAGAAATTCAAAAAAGATGTCGTTGCGTAATCGGTAAA
GATTATCCCGAGCCAATGATTGATTTAAATCGAGCGATGCAAATTAATTCAAGTCGTATG
AAAGAAATTAGAAATTCATTGATTGAAGTCAAACAACCACATGTGCGACCATCAAATGAA
GATGAAATTCGTACATTCTTTTGGATAGCTGACGATATTGCTGTCAAGTGTTAA
>g12075.t1 Gene=g12075 Length=537
MEVKSIIWFRHGLRIHDNPALLEAIKSEGSSKVTFYPVFIFDGITAGTKLVGYNRMKFLI
ESLEDLNEQFKSFGGNGLHIFRGDPVEIFTKLSKELGINKICFEQDCEPIWNERDMRVAQ
MCKELDITLIEKISHTLWDPNSVINANGGYPPLTYQMFLHTVNVLGNPSRPVQMPCFSNV
VFGTIPLHLHKQLGLMNSIPSPEDFSLFPSKSKKFLVWKGGEKRALEQLKIRLQVEQEAF
LNGTYLPNQGNPKLTGDSTSMSAALRFGCLSVRKFFYDIHDLFAEVKQKTFSNTPGGHHI
TGQLIWREYFYTMSVRNPFYAQMENNPICLNINWSRPNDEDILKWKEGRTGFPIIDASMR
QILSEGWIHHTLRNITATFLTRTGLWYSWEIGLQHFLKYLLDADWSVCSGNWLWVSSSAF
ERLLDSSKFSIIAIAYRLDPEGTYIRRYIRELRDIPNRYIHEPWKTPLEIQKRCRCVIGK
DYPEPMIDLNRAMQINSSRMKEIRNSLIEVKQPHVRPSNEDEIRTFFWIADDIAVKC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g12075.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 2 | 134 | 6.2E-36 |
| 12 | g12075.t1 | Gene3D | G3DSA:1.10.579.10 | DNA Cyclobutane Dipyrimidine Photolyase | 318 | 531 | 7.5E-79 |
| 3 | g12075.t1 | PANTHER | PTHR11455 | CRYPTOCHROME | 4 | 532 | 7.2E-229 |
| 4 | g12075.t1 | PANTHER | PTHR11455:SF17 | CRYPTOCHROME-1 | 4 | 532 | 7.2E-229 |
| 7 | g12075.t1 | PRINTS | PR00147 | DNA photolyase signature | 350 | 366 | 5.3E-7 |
| 6 | g12075.t1 | PRINTS | PR00147 | DNA photolyase signature | 370 | 388 | 5.3E-7 |
| 5 | g12075.t1 | PRINTS | PR00147 | DNA photolyase signature | 410 | 424 | 5.3E-7 |
| 2 | g12075.t1 | Pfam | PF00875 | DNA photolyase | 5 | 163 | 1.8E-38 |
| 1 | g12075.t1 | Pfam | PF03441 | FAD binding domain of DNA photolyase | 302 | 501 | 1.7E-64 |
| 10 | g12075.t1 | ProSitePatterns | PS00394 | DNA photolyases class 1 signature 1. | 350 | 362 | - |
| 13 | g12075.t1 | ProSiteProfiles | PS51645 | Photolyase/cryptochrome alpha/beta domain profile. | 3 | 137 | 32.411 |
| 8 | g12075.t1 | SUPERFAMILY | SSF52425 | Cryptochrome/photolyase, N-terminal domain | 5 | 175 | 2.75E-45 |
| 9 | g12075.t1 | SUPERFAMILY | SSF48173 | Cryptochrome/photolyase FAD-binding domain | 206 | 505 | 2.35E-81 |
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 transcript has been annotated with K02295 (cryptochrome)
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.
