General information for g11044.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cryptochrome-1.
Parent gene
- The parent gene g11044 is located on chr_1: 13656860..13657628 (- 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 | g11044 | g11044.t1 | TTS | g11044.t1 | 13652493 | 13652493 |
| chr_1 | g11044 | g11044.t1 | isoform | g11044.t1 | 13652614 | 13656977 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon1 | 13652614 | 13653092 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS1 | 13652614 | 13653092 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon2 | 13653147 | 13653292 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS2 | 13653147 | 13653292 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon3 | 13653347 | 13654031 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS3 | 13653347 | 13654031 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon4 | 13654084 | 13654185 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS4 | 13654084 | 13654185 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon5 | 13654526 | 13654668 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS5 | 13654526 | 13654668 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon6 | 13654736 | 13654987 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS6 | 13654736 | 13654987 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon7 | 13656344 | 13656467 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS7 | 13656344 | 13656467 |
| chr_1 | g11044 | g11044.t1 | exon | g11044.t1.exon8 | 13656860 | 13656977 |
| chr_1 | g11044 | g11044.t1 | cds | g11044.t1.CDS8 | 13656860 | 13656977 |
| chr_1 | g11044 | g11044.t1 | TSS | g11044.t1 | 13657628 | 13657628 |
Sequences
>g11044.t1 Gene=g11044 Length=2049
ATGACGATGACAGCTGGAAGTAATCAAAATAATCAATCTAATGTTGGAAATGCACAAACA
CAGCAACAACAACAAAAACCACAAAAAGAAAAGCATTTGGTTCATTGGTTTAGAAAAGGT
TTAAGGCTTCATGACAACCCTGCATTGAGAGAAGGATTAAAAAATGCAACAACTTTTCGA
TGTATCTTTCTGGTAGATCCATGGTTTGCTGGTTCATCTAATGTTGGTATAAATAAATGG
AGATTCTTGTTACAATGCTTAGAAGACCTTGATAAAAGTCTAAGACGATTGAATTCTCGT
TTATTTGTTATACGTGGTCAACCAGCTGAAAAACTACCATTGCTGTTTAAGAAATGGAAT
ACAACATGTCTTACATTTGAAGAAGATCCTGAGCCATTTAGTCGTGTTCGAGATCACAAC
ATCACAGAAATGTGCAAAGAACTTAAAATAGAAGTGATCACAGCCGTGTCTCATACTCTG
TACAAATTAGAAAAAATAATTGAGAAAAATAATGATAAGCCACCGTTGACATATCATCAA
TTTCAAGCAATTATTTCGTCAATGGATCCTCCTCCACAACCTGCAGAGACAGTCACTGAA
GAAACAATTGGAAATTCTCGAACTCCTATTCATGAAGATCATGAAGAGAAATATGGAGTG
CCGACGCTTGAAGAATTGGGATTTGAAACTGACAATCTTAAACCAGCTGTGTGGATAGGC
GGTGAAAGTGAAGCTCTTGCACGTTTAGAAAGACATCTTGAAAGAAAAGCTTGGGTCGCA
AGCTTTGGAAGACCAAAAATGTCACCTCAATCTCTGCTAGCATCACAAACTGGTCTTTCA
CCTTATCTTCGTTTTGGCTGTCTCTCAACGCGACTCTTTTATTATCAATTGACTGACTTG
TATAAGAAAATTAAGAAAACAAACCCGCCACTCAGTTTACATGGTCAATTATTATGGAGA
GAATTTTTCTATTGTTGCTCAACAAAAAATCCAAATTTTGATAAGATGGTTGGCAATCCA
ATTTGCGTGCAAATTCCATGGGACAAAAATCCTGAAGCACTTGCAAAATGGGCAAATGGT
CAAACAGGCTATCCTTGGATTGATGCCATAATGAATCAATTGCGTGAAGAAGGCTGGATT
CATCATTTAGCGAGACATGCAGTTGCATGCTTTCTCACTCGAGGAAATTTATGGATATCA
TGGGAAGAAGGCATGAAAGTTTTTGAAGAACTTTTATTGGACGCAGATTGGTCAGTTAAT
GCAGGAATGTGGTTGTGGTTGAGTTGTTCCTCATTTTTTCAACAATTCTTTCACTGTTAT
TGTCCTGTCAAGTTTGGAAGAAAAGCTGACCCAAATGGAGACTATATTCGTCGTTACATC
CCTGCATTAAAAAATTTTCCAACAAAATACATTCATGAACCATGGGTTGCTTCAGAGCTT
GTTCAAAAAAATGCTAAATGCATAATTGGCAAAGATTATCCATTAGCAATGATTAATCAC
GTGACAGCAAGCAAGACAAATATGGAAAGAATGAAACAAGTTTATCAGCAACTTGCAAAA
TATCGAAATACTTATATAAATCCAGATGGTGGAGGGTCAGCGATCTCAAGTATGCTAGCA
AAAGCTCAAGCATCAGCTTTAGTAAATGCTGAACAACAAAATAGCAGTCCTTCACCAACG
ACAATTTTAAAATCAGTAAATAGCTCTGGTAGCTATATGTGCTCGACGACACGCTCAAAT
TTAGAGATGCAATCACCATCACCAGTTGTTATTTATCACGAATCCTCAAATTCATCTCTC
ATGACACAAATGCAGCATCGAAACGCTAACAATATGATTCGCATGAACAAAAATCACAAT
CGTTTTAACTTTGATGATAATGATGAGAACGAAAATCAACAAAATCAAGTTCAGTTTCAC
AATGCATACAACAATTACACAACAAATCAGCATCAAGTCATATCAGAAATGCAACAACAA
GCCGATCAACAAACAGAAATCGAATTGAGAATGAATAATCTTGGTAATGAGAGGCAGGAT
GTTGAATAA
>g11044.t1 Gene=g11044 Length=682
MTMTAGSNQNNQSNVGNAQTQQQQQKPQKEKHLVHWFRKGLRLHDNPALREGLKNATTFR
CIFLVDPWFAGSSNVGINKWRFLLQCLEDLDKSLRRLNSRLFVIRGQPAEKLPLLFKKWN
TTCLTFEEDPEPFSRVRDHNITEMCKELKIEVITAVSHTLYKLEKIIEKNNDKPPLTYHQ
FQAIISSMDPPPQPAETVTEETIGNSRTPIHEDHEEKYGVPTLEELGFETDNLKPAVWIG
GESEALARLERHLERKAWVASFGRPKMSPQSLLASQTGLSPYLRFGCLSTRLFYYQLTDL
YKKIKKTNPPLSLHGQLLWREFFYCCSTKNPNFDKMVGNPICVQIPWDKNPEALAKWANG
QTGYPWIDAIMNQLREEGWIHHLARHAVACFLTRGNLWISWEEGMKVFEELLLDADWSVN
AGMWLWLSCSSFFQQFFHCYCPVKFGRKADPNGDYIRRYIPALKNFPTKYIHEPWVASEL
VQKNAKCIIGKDYPLAMINHVTASKTNMERMKQVYQQLAKYRNTYINPDGGGSAISSMLA
KAQASALVNAEQQNSSPSPTTILKSVNSSGSYMCSTTRSNLEMQSPSPVVIYHESSNSSL
MTQMQHRNANNMIRMNKNHNRFNFDDNDENENQQNQVQFHNAYNNYTTNQHQVISEMQQQ
ADQQTEIELRMNNLGNERQDVE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g11044.t1 | Gene3D | G3DSA:3.40.50.620 | HUPs | 30 | 157 | 6.0E-45 |
| 11 | g11044.t1 | Gene3D | G3DSA:1.25.40.80 | - | 159 | 206 | 2.2E-7 |
| 10 | g11044.t1 | Gene3D | G3DSA:1.25.40.80 | - | 207 | 330 | 1.7E-38 |
| 12 | g11044.t1 | Gene3D | G3DSA:1.10.579.10 | DNA Cyclobutane Dipyrimidine Photolyase | 331 | 554 | 1.1E-87 |
| 7 | g11044.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 27 | - |
| 8 | g11044.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 29 | - |
| 3 | g11044.t1 | PANTHER | PTHR11455:SF30 | CRYPTOCHROME 2 | 24 | 527 | 3.5E-296 |
| 4 | g11044.t1 | PANTHER | PTHR11455 | CRYPTOCHROME | 24 | 527 | 3.5E-296 |
| 2 | g11044.t1 | Pfam | PF00875 | DNA photolyase | 34 | 191 | 5.1E-41 |
| 1 | g11044.t1 | Pfam | PF03441 | FAD binding domain of DNA photolyase | 315 | 513 | 1.0E-76 |
| 13 | g11044.t1 | ProSiteProfiles | PS51645 | Photolyase/cryptochrome alpha/beta domain profile. | 31 | 160 | 35.983 |
| 5 | g11044.t1 | SUPERFAMILY | SSF52425 | Cryptochrome/photolyase, N-terminal domain | 29 | 218 | 1.96E-50 |
| 6 | g11044.t1 | SUPERFAMILY | SSF48173 | Cryptochrome/photolyase FAD-binding domain | 225 | 516 | 3.79E-93 |
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.
