General information for g13877.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Riboflavin kinase.
Parent gene
- The parent gene g13877 is located on chr_1: 33087875..33088389 (+ 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 | g13877 | g13877.t1 | TSS | g13877.t1 | 33087109 | 33087109 |
| chr_1 | g13877 | g13877.t1 | isoform | g13877.t1 | 33087189 | 33088129 |
| chr_1 | g13877 | g13877.t1 | exon | g13877.t1.exon1 | 33087189 | 33087279 |
| chr_1 | g13877 | g13877.t1 | cds | g13877.t1.CDS1 | 33087189 | 33087279 |
| chr_1 | g13877 | g13877.t1 | exon | g13877.t1.exon2 | 33087369 | 33087380 |
| chr_1 | g13877 | g13877.t1 | cds | g13877.t1.CDS2 | 33087369 | 33087380 |
| chr_1 | g13877 | g13877.t1 | exon | g13877.t1.exon3 | 33087456 | 33087607 |
| chr_1 | g13877 | g13877.t1 | cds | g13877.t1.CDS3 | 33087456 | 33087607 |
| chr_1 | g13877 | g13877.t1 | exon | g13877.t1.exon4 | 33087857 | 33088129 |
| chr_1 | g13877 | g13877.t1 | cds | g13877.t1.CDS4 | 33087857 | 33088129 |
| chr_1 | g13877 | g13877.t1 | TTS | g13877.t1 | 33088373 | 33088373 |
Sequences
>g13877.t1 Gene=g13877 Length=528
ATGAGAAATTTAAGTAAAGTTGTTTCAGGACTTCCACATTTTGCTTGTGGTCAAATTATA
AAAGGATTTGGTCGAGGATCAAAACAATTAGGCATTCCAACTGCCAACTATCCACTCGAG
GTCGTCGAAAATTTACCTAAAGAGCTCAGCACAGGTATCTACTATGGATATGCAAGTATA
GACAATGGTGAAGTACATAAAATGGTCATGTCAATTGGAATGAATCCTTATTTTGAAAAC
AAACACAAGTCAATGGAAACACACATTCTGCACAACTTTATGGGAGATCTATATGGACAT
ATTTTAAAAGTATGCATTGTTGGATACTTAAGGCCGGAAAAAAATTTCGACAGTTTAGAA
GCATTAATTGACGCAATTAAAAAGGATATAAGTGATGCAGAGAAATTATTAGACAACCCT
GAAAATTTGCAGTTCAGAAATCATGAATTCTTCAAAGAAACGATAAATGGACAAATTTTG
ATAAACGGTCATCATAAAAATGGTACAAAAATTAATGGGCATATCTAA
>g13877.t1 Gene=g13877 Length=175
MRNLSKVVSGLPHFACGQIIKGFGRGSKQLGIPTANYPLEVVENLPKELSTGIYYGYASI
DNGEVHKMVMSIGMNPYFENKHKSMETHILHNFMGDLYGHILKVCIVGYLRPEKNFDSLE
ALIDAIKKDISDAEKLLDNPENLQFRNHEFFKETINGQILINGHHKNGTKINGHI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g13877.t1 | Coils | Coil | Coil | 116 | 136 | - |
| 6 | g13877.t1 | Gene3D | G3DSA:2.40.30.30 | - | 9 | 155 | 5.7E-57 |
| 2 | g13877.t1 | PANTHER | PTHR22749 | RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE | 6 | 157 | 1.8E-68 |
| 3 | g13877.t1 | PANTHER | PTHR22749:SF6 | RIBOFLAVIN KINASE | 6 | 157 | 1.8E-68 |
| 1 | g13877.t1 | Pfam | PF01687 | Riboflavin kinase | 12 | 137 | 3.9E-42 |
| 5 | g13877.t1 | SMART | SM00904 | Flavokinase_2 | 8 | 138 | 5.7E-41 |
| 4 | g13877.t1 | SUPERFAMILY | SSF82114 | Riboflavin kinase-like | 10 | 153 | 3.49E-45 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0009231 | riboflavin biosynthetic process | BP |
| GO:0008531 | riboflavin kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00861 (riboflavin kinase)
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.
