General information for g6063.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cryptochrome-1.
Parent gene
- The parent gene g6063 is located on chr_2: 13969764..13971562 (- 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 | g6063 | g6063.t1 | TTS | g6063.t1 | 13969726 | 13969726 |
| chr_2 | g6063 | g6063.t1 | isoform | g6063.t1 | 13969764 | 13971562 |
| chr_2 | g6063 | g6063.t1 | exon | g6063.t1.exon1 | 13969764 | 13970173 |
| chr_2 | g6063 | g6063.t1 | cds | g6063.t1.CDS1 | 13969764 | 13970173 |
| chr_2 | g6063 | g6063.t1 | exon | g6063.t1.exon2 | 13970242 | 13971212 |
| chr_2 | g6063 | g6063.t1 | cds | g6063.t1.CDS2 | 13970242 | 13971212 |
| chr_2 | g6063 | g6063.t1 | exon | g6063.t1.exon3 | 13971276 | 13971406 |
| chr_2 | g6063 | g6063.t1 | cds | g6063.t1.CDS3 | 13971276 | 13971406 |
| chr_2 | g6063 | g6063.t1 | exon | g6063.t1.exon4 | 13971461 | 13971562 |
| chr_2 | g6063 | g6063.t1 | cds | g6063.t1.CDS4 | 13971461 | 13971562 |
| chr_2 | g6063 | g6063.t1 | TSS | g6063.t1 | 13971638 | 13971638 |
Sequences
>g6063.t1 Gene=g6063 Length=1614
ATGGCTTCAAAAACTACTGTAATTCATTGGTTTCGTAAAGGACTACGAGTGCATGATAAT
CCAGCATTAGTGCGTGCAGTAGAAGAAGCTATATCTCGAAAATCTTATTTTAGAGCAATA
TTTATGTTAGATCCTGGTATTTTATCGTGGATGACAGTTGGACCTAATCGTTGGCGATTT
TTACAAGAAACACTCTCTGATTTGGACGAAAACTTAAAAAAAATTAATTCAAGACTGTAT
GTGATAAGAGGAAATCCAAATGAGACTTTTCCAAAACTATTTAAATTGTGGAATGTAGAA
CTTTTAACTTTTGAACATGACATTGAGCCATATTCAATAGAAAGAGATGAGATTGTCAAG
AATCAAGCAGAAAAATTTAATGTTGAAGTTATTGAAGAATACTCTTTGACAATCTTCAAT
CCAGAGCTTGTTGTTCAAAAAAATCGTGGTTCAACTCCAATGACTTATCAAAAGTTTCTT
TCAGTTGCAAGTGAATTGAAAGTACCACAACCTGTCGACAATCCTACAAAGTTACCAAAC
TCATGTATTCCTGAACTTGACAAAAATGAATTGAAAGATGAAGAAGTTTATGATGTGCCT
ACACTCGAGCAACTTGGTGTCAATTCATCCGAAATTAGTGAATATTCACGTTTTCCTGGT
GGTGAAACAGAAGCTTTGAGAAGAATGAATGAAAAATTGAAAGATGTTAAATTTATTTGT
GAATTTGAGAAGCCTAATACATCACCAAACTCTTTAGAGCCATCAACAACAGTTCTCTCA
CCATATTTAAAGTTTGGTGCTCTTAGTGCTCGTTTGTTCTATCAAAAGATTAAGGAAGTA
TATCGAGGAAGAAAGCATTCAAGTCCTCCTGTGTCGCTCGAAGGTCAATTAATTTGGCGA
GAATTTTATTATACAGTTGCTGCAACAACAGAAAACTATGATCGAATGGTAGGGAATAAA
ATTTGTACACAAATTCCATGGAAAACAAATCCTAAATATCTCGAAGCTTGGAAGAACGGA
CGAAGTGGATATCCTTTTATTGATGCAATCATGCGTCAGCTCAAACAAGAGGGATGGATA
CATCATTTAGGACGTCATGCTGTTGCTTGTTTTTTAACAAGAGGCGATCTTTGGTGCTCA
TGGGAAGATGGTGTAAAAGTTTTTGAAGAATTTTTGCTCGATGCTGATTGGGCATTAAAC
ACAGGTAATTGGTTATGGCTATCTGCAAGTGCCTTTTTCCATCAATATTATCGTGTATAT
TCACCAATTGCTTTTGGGAAAAAGACTGATCCAGAGGGAAAATACATCAAAAAATATGTG
CCTGAACTTAGGAAATATCCAAGTGGCAGTATTTATGAACCATGGAAAGTTTCACTTGAA
AATCAAAAGAAATATGGATGTGTTATTGGAACAGACTATCCACATCGAATTGTTATACAC
GAAGATGCTATGAAAGAAAATTTAAGCAGAATGAAAGCTGCATATGCAAAGAAGAAAGTT
GACGTTGAAGAAACTCCTCAAGGAAAACGAAAGGCTGATTCACCAAAAGGTAATACAAGT
AAAAAAGCTGCTACCAAACAACGAAACTCGTTAGAAAAATATTTTAAAAAATAA
>g6063.t1 Gene=g6063 Length=537
MASKTTVIHWFRKGLRVHDNPALVRAVEEAISRKSYFRAIFMLDPGILSWMTVGPNRWRF
LQETLSDLDENLKKINSRLYVIRGNPNETFPKLFKLWNVELLTFEHDIEPYSIERDEIVK
NQAEKFNVEVIEEYSLTIFNPELVVQKNRGSTPMTYQKFLSVASELKVPQPVDNPTKLPN
SCIPELDKNELKDEEVYDVPTLEQLGVNSSEISEYSRFPGGETEALRRMNEKLKDVKFIC
EFEKPNTSPNSLEPSTTVLSPYLKFGALSARLFYQKIKEVYRGRKHSSPPVSLEGQLIWR
EFYYTVAATTENYDRMVGNKICTQIPWKTNPKYLEAWKNGRSGYPFIDAIMRQLKQEGWI
HHLGRHAVACFLTRGDLWCSWEDGVKVFEEFLLDADWALNTGNWLWLSASAFFHQYYRVY
SPIAFGKKTDPEGKYIKKYVPELRKYPSGSIYEPWKVSLENQKKYGCVIGTDYPHRIVIH
EDAMKENLSRMKAAYAKKKVDVEETPQGKRKADSPKGNTSKKAATKQRNSLEKYFKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g6063.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 8 | 220 | 5.2E-97 |
| 10 | g6063.t1 | Gene3D | G3DSA:1.25.40.80 | - | 136 | 304 | 5.2E-97 |
| 11 | g6063.t1 | Gene3D | G3DSA:1.10.579.10 | DNA Cyclobutane Dipyrimidine Photolyase | 311 | 534 | 4.9E-87 |
| 7 | g6063.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 499 | 537 | - |
| 8 | g6063.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 499 | 517 | - |
| 3 | g6063.t1 | PANTHER | PTHR11455 | CRYPTOCHROME | 6 | 526 | 9.0E-207 |
| 4 | g6063.t1 | PANTHER | PTHR11455:SF52 | CRYPTOCHROME CIRCADIAN REGULATOR 5 | 6 | 526 | 9.0E-207 |
| 2 | g6063.t1 | Pfam | PF00875 | DNA photolyase | 7 | 171 | 8.8E-40 |
| 1 | g6063.t1 | Pfam | PF03441 | FAD binding domain of DNA photolyase | 295 | 492 | 4.4E-75 |
| 12 | g6063.t1 | ProSiteProfiles | PS51645 | Photolyase/cryptochrome alpha/beta domain profile. | 5 | 138 | 35.024 |
| 5 | g6063.t1 | SUPERFAMILY | SSF52425 | Cryptochrome/photolyase, N-terminal domain | 6 | 222 | 1.3E-46 |
| 6 | g6063.t1 | SUPERFAMILY | SSF48173 | Cryptochrome/photolyase FAD-binding domain | 211 | 496 | 2.75E-92 |
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.
