General information for g6652.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Xanthine dehydrogenase.
Parent gene
- The parent gene g6652 is located on chr_2: 17947216..17949166 (+ 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 | g6652 | g6652.t2 | TSS | g6652.t2 | 17943454 | 17943454 |
| chr_2 | g6652 | g6652.t2 | isoform | g6652.t2 | 17944343 | 17947006 |
| chr_2 | g6652 | g6652.t2 | exon | g6652.t2.exon1 | 17944343 | 17944390 |
| chr_2 | g6652 | g6652.t2 | cds | g6652.t2.CDS1 | 17944343 | 17944390 |
| chr_2 | g6652 | g6652.t2 | exon | g6652.t2.exon2 | 17944675 | 17947006 |
| chr_2 | g6652 | g6652.t2 | cds | g6652.t2.CDS2 | 17944675 | 17947005 |
| chr_2 | g6652 | g6652.t2 | TTS | g6652.t2 | NA | NA |
Sequences
>g6652.t2 Gene=g6652 Length=2380
ATGACTTCAATCAACTCGAATTTAATATTTTTCGTTAATGGTAAAAAGGTAATTGAAACG
AAACCAAATCCAGAGATAACGTTACTTCGATATTTACGCGAGAAACTCAAATTAAGTGGT
ACAAAATTGGGATGCGCTGAAGGTGGCTGTGGTGCTTGTACTGTGATGGTTTCAAAGTTC
AATAGAGATACCAATGTCGTTAATCATTTTTCAGTTAATGCATGTTTAATGCCAGTATGT
GCTTTACATGGTTTAGCTGTTACCACTGTTGAGGGAATTGGAAGTACCAGAACTCGATTG
CATCCAGTACAAGAGAGAATCGCTAAAGCTCATGGTTCGCAATGTGGTTTTTGTACTCCA
GGAATTGTCATGTCAATGTACTCGTTACTAAGAAATTCTTCAAAACCATCTATGAAAGAA
CTAGAAATTGCTATGCAAGGAAATTTATGTCGATGTACTGGCTATCGTCCAATCATTGAA
GGATTTCGTACATTCACGAAAGAATATGAGACATGTGATATGGGTGATGCATGTTGTAAA
AAAAACAAACAAGGATGTAACGCTACTTTAGTAGATGACAAATTGTTTAATTCGAGCGAA
TTTGTACCATATGATCACTCACAAGAACCAATATTTCCTCCTGAACTTAAATTAGTTGAT
CAATATGATAAAGAATCATTATATTTTGAAAATGATCGTGGAATAATCTGGTTTAGACCT
ACTCAACTACATCAATTACTAGAATTTAAGCAGCAACATAAAACAGCTGCCAAAATTGTA
GTTGGAAATACTGAAGTTGGTGTTGAAGTAAAATTCAAACATTTCGATTACAAATTCTTT
GCTAATCCATCGCATATTCGTGAATTAAACGAACTGACAGTCACTGAAAATGGTTTAAAA
GTTGGAGCTGCTGTGACTTTGACTCAACTAAAGAATTTCATTGACGCAAAATTAAACTGT
AATCCAATTGAAATTTCGATTTTAGATATGCTGCATTGGTTTGCAGGCACACAAGTTCGC
AATGTAGCTTCAATTGGTGGAAATTTAATGACAAGTTCGCCTATATCTGATTTAAATCCA
ATTTTGCTTGCTGCAAATGCTGAATTGGAAGTTCAAAGTTTTGATAATGGAAAGAGAATT
ATAAAAATGGATGAAAATTTTTTCACTGGTTATCGTAAGAATTCAATTAAAGACAACGAA
GTTTTAATTTCAATTTTAATTCCTAATACAATCGATAACCAACATTTTGTGGCTTATAAA
CAAGCAAAAAGACGTGAAGATGATATTGCAATTGTCACAGCAGCTTTTAATTTTATATTT
AAAACTGACACAAATATTATTGAAAAAGCAAATTTTGTTTTCGGTGGAATGGCACCAACA
ACAATTTTGGCACCTAAAACTGCAGCATTAGTGAAAGGAAAAGAATGGAATCGAGAATTG
ATTGAAATTGTTAATCAAAGTTTGGTTGATGAAATTCCTTTATCTTTTGATGCACCGGGT
GGAAGCGTTCTATATAGAAAATCACTTACTTTGAGTTTATTCTTTAAAGCATTTTTAAAA
ATTAGCAATGATCTTGAAAAATCTCAAAATATAAGTATTTTAAATGAACGTGAGAGAAGC
GGAATTGGTGGTTTTAAAACATTAGTTCCAAAAAGCTCACAATTATTTGAAAAAGTTTCG
AGTGATCAATCACTTACAGACCCTATTTACCGACCAAAAGTGCATATGTCAGCTCTAAAA
CAAGCAACTGGTGAAGCAATTTATTGTGATGATATACCCAAATATGAAAATGAACTTTAT
CTTGCATTGGTGTTGAGCACAAAAGCACATGCAAAAATTTTAGCAATTGACGAGAGTGAA
GCATTGAAACAGCCAGGTGTTTATGCATTTTTCTCAGCAAAAGATTTAACGTCAAATCAA
AATAAAATTGGGCCGGTATTTCATGATGAAGAATTATTCATAAGAGAAACTGTAACAAGT
CAAGGACAAATTTTGGGTGTAATTGTCGGTGAAGATCAAAATGTAGTTCAAAAAGCTGCA
AGGCTAGTGAAAATACAATATGAAGAATTGAGTCCAATAATTGTTACAATTGAAGATGCT
ATAAAACATAACTCTGTATTTCCTGGCTATCCAAAATTCCTTATTAATGGAGATGTTGAT
AAAGCTTTCAATGAAGCTGATCATGTTTTAGAAGGAGAAATTCGTTTGGGTGGTCAAGAA
CATTTTTATTTAGAAACGCATGCGGCAATAGCAATTCCAAAAGATGGAGACGAAATTGAA
ATAATAGCATCTACACAACATCCTTCTGAAATTGCAAAACTGGCTGCTCATGTATTAGGA
ATTCCAAATAATCGTGTAGTTTGTAAAACAAAAAGATTAG
>g6652.t2 Gene=g6652 Length=793
MTSINSNLIFFVNGKKVIETKPNPEITLLRYLREKLKLSGTKLGCAEGGCGACTVMVSKF
NRDTNVVNHFSVNACLMPVCALHGLAVTTVEGIGSTRTRLHPVQERIAKAHGSQCGFCTP
GIVMSMYSLLRNSSKPSMKELEIAMQGNLCRCTGYRPIIEGFRTFTKEYETCDMGDACCK
KNKQGCNATLVDDKLFNSSEFVPYDHSQEPIFPPELKLVDQYDKESLYFENDRGIIWFRP
TQLHQLLEFKQQHKTAAKIVVGNTEVGVEVKFKHFDYKFFANPSHIRELNELTVTENGLK
VGAAVTLTQLKNFIDAKLNCNPIEISILDMLHWFAGTQVRNVASIGGNLMTSSPISDLNP
ILLAANAELEVQSFDNGKRIIKMDENFFTGYRKNSIKDNEVLISILIPNTIDNQHFVAYK
QAKRREDDIAIVTAAFNFIFKTDTNIIEKANFVFGGMAPTTILAPKTAALVKGKEWNREL
IEIVNQSLVDEIPLSFDAPGGSVLYRKSLTLSLFFKAFLKISNDLEKSQNISILNERERS
GIGGFKTLVPKSSQLFEKVSSDQSLTDPIYRPKVHMSALKQATGEAIYCDDIPKYENELY
LALVLSTKAHAKILAIDESEALKQPGVYAFFSAKDLTSNQNKIGPVFHDEELFIRETVTS
QGQILGVIVGEDQNVVQKAARLVKIQYEELSPIIVTIEDAIKHNSVFPGYPKFLINGDVD
KAFNEADHVLEGEIRLGGQEHFYLETHAAIAIPKDGDEIEIIASTQHPSEIAKLAAHVLG
IPNNRVVCKTKRL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g6652.t2 | CDD | cd00207 | fer2 | 9 | 88 | 1.12265E-7 |
| 15 | g6652.t2 | Gene3D | G3DSA:3.30.365.10 | Aldehyde Oxidoreductase; domain 4 | 4 | 793 | 1.1E-299 |
| 7 | g6652.t2 | PANTHER | PTHR11908 | XANTHINE DEHYDROGENASE | 2 | 793 | 1.7E-255 |
| 8 | g6652.t2 | PANTHER | PTHR11908:SF86 | ALDEHYDE OXIDASE | 2 | 793 | 1.7E-255 |
| 3 | g6652.t2 | Pfam | PF00111 | 2Fe-2S iron-sulfur cluster binding domain | 11 | 79 | 1.8E-8 |
| 5 | g6652.t2 | Pfam | PF01799 | [2Fe-2S] binding domain | 89 | 161 | 1.3E-29 |
| 1 | g6652.t2 | Pfam | PF00941 | FAD binding domain in molybdopterin dehydrogenase | 237 | 409 | 1.2E-46 |
| 4 | g6652.t2 | Pfam | PF03450 | CO dehydrogenase flavoprotein C-terminal domain | 418 | 520 | 5.0E-29 |
| 6 | g6652.t2 | Pfam | PF01315 | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain | 583 | 690 | 8.9E-35 |
| 2 | g6652.t2 | Pfam | PF02738 | Molybdopterin-binding domain of aldehyde dehydrogenase | 715 | 792 | 7.4E-25 |
| 17 | g6652.t2 | ProSitePatterns | PS00197 | 2Fe-2S ferredoxin-type iron-sulfur binding region signature. | 45 | 53 | - |
| 22 | g6652.t2 | ProSiteProfiles | PS51085 | 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. | 6 | 93 | 10.3 |
| 21 | g6652.t2 | ProSiteProfiles | PS51387 | PCMH-type FAD-binding domain profile. | 230 | 412 | 20.905 |
| 18 | g6652.t2 | SMART | SM01092 | CO_deh_flav_C_2 | 417 | 521 | 2.1E-25 |
| 19 | g6652.t2 | SMART | SM01008 | Ald_Xan_dh_C_2 | 583 | 691 | 7.5E-39 |
| 14 | g6652.t2 | SUPERFAMILY | SSF54292 | 2Fe-2S ferredoxin-like | 8 | 93 | 2.57E-22 |
| 10 | g6652.t2 | SUPERFAMILY | SSF47741 | CO dehydrogenase ISP C-domain like | 101 | 214 | 3.66E-35 |
| 13 | g6652.t2 | SUPERFAMILY | SSF56176 | FAD-binding/transporter-associated domain-like | 193 | 408 | 2.07E-59 |
| 9 | g6652.t2 | SUPERFAMILY | SSF55447 | CO dehydrogenase flavoprotein C-terminal domain-like | 413 | 525 | 6.15E-34 |
| 12 | g6652.t2 | SUPERFAMILY | SSF54665 | CO dehydrogenase molybdoprotein N-domain-like | 565 | 707 | 4.71E-38 |
| 11 | g6652.t2 | SUPERFAMILY | SSF56003 | Molybdenum cofactor-binding domain | 692 | 792 | 3.79E-26 |
| 20 | g6652.t2 | TIGRFAM | TIGR02963 | xanthine_xdhA: xanthine dehydrogenase, small subunit | 9 | 520 | 1.0E-160 |
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:0009055 | electron transfer activity | MF |
| GO:0051537 | 2 iron, 2 sulfur cluster binding | MF |
| GO:0004855 | xanthine oxidase activity | MF |
| GO:0050660 | flavin adenine dinucleotide binding | MF |
| GO:0004854 | xanthine dehydrogenase activity | MF |
| GO:0055114 | NA | NA |
| GO:0051536 | iron-sulfur cluster binding | MF |
| GO:0046872 | metal ion binding | MF |
| GO:0071949 | FAD binding | MF |
| GO:0016491 | oxidoreductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K03518 (aerobic carbon-monoxide dehydrogenase small subunit)
Pathway
This gene does not belong to any 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.
