General information for g9324.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Xanthine dehydrogenase.
Parent gene
- The parent gene g9324 is located on chr_1: 1859182..1862985 (+ 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 | g9324 | g9324.t1 | isoform | g9324.t1 | 1859182 | 1862985 |
| chr_1 | g9324 | g9324.t1 | exon | g9324.t1.exon1 | 1859182 | 1859232 |
| chr_1 | g9324 | g9324.t1 | cds | g9324.t1.CDS1 | 1859182 | 1859232 |
| chr_1 | g9324 | g9324.t1 | exon | g9324.t1.exon2 | 1859285 | 1861604 |
| chr_1 | g9324 | g9324.t1 | cds | g9324.t1.CDS2 | 1859285 | 1861604 |
| chr_1 | g9324 | g9324.t1 | exon | g9324.t1.exon3 | 1861796 | 1862107 |
| chr_1 | g9324 | g9324.t1 | cds | g9324.t1.CDS3 | 1861796 | 1862107 |
| chr_1 | g9324 | g9324.t1 | exon | g9324.t1.exon4 | 1862165 | 1862985 |
| chr_1 | g9324 | g9324.t1 | cds | g9324.t1.CDS4 | 1862165 | 1862985 |
| chr_1 | g9324 | g9324.t1 | TSS | g9324.t1 | NA | NA |
| chr_1 | g9324 | g9324.t1 | TTS | g9324.t1 | NA | NA |
Sequences
>g9324.t1 Gene=g9324 Length=3504
ATGAATACAGAAAATGAAAAAAATTTGGTGTTTTTTGTCAATGGAAAGAAGATAACAGAA
AATGAACCAGATCCAGAAATCACTTTGCTTCGTTATCTTCGTGAAAAATTGAAATTAACA
GGCACGAAATTGGGTTGTTCTGAAGGTGGATGTGGTGCTTGTACTGTGATGATTTCGAAG
TTCAATCGTGAAACAAACAAAGTTCAACATTTTTCAGCCAATGCATGTTTGATGCCAGTC
TGTGCTTTACATGGATTGGCTGTAACAACTGTTGAAGGAATTGGCAGCACAAGAGATCGA
TTGCATCCAGTTCAAGAGAGAATTGCTAAAGCTCATGGTTCACAATGTGGTTTCTGTACA
CCTGGCATGGTCATGTCAATGTATGCACTACTTAGAAATTCATCAAAACCATCAATGAAA
GAACTTGAAATTGCAATGCAAGGAAACTTGTGTCGATGCACTGGCTATCGACCAATCATT
GAAGGTTATCGAACATTTACAAAAGAATTCGGCAATGAAGAAGTTTGTGGAATGGGTGAA
AAATGTTGCAAAGTCAATGGAGGAAAATTGGTTGATGACAAATTATTTGAAGTCAGTGAA
TTTGTGCCTTATAATCCATCACAAGAACCAATTTTTCCACCTGAATTAAAACTCAATGAT
CAATTTGATAAGGAAACATTGAAATTTATAAATGATCGTGATGTGATGTGGTTCAGACCA
ATTGAATTAAAAGAATTATTGAAATTCAAACAAGAACATGGAACAGCAGCAAAAATTGTT
GTTGGAAACACTGAAGTCGGTGTTGAAGTAAAATTTAAAAATTTTGATTATAAATTCTTG
GCAAATCCATCACAAATACGAGAACTAAATGAACTAGAAGTCACAAAAGATGGTTTGAAA
ATTGGAGCTGCTGTGACTTTGACTGAGATTGAAAATTTCATTGAAAGTAAAACAGACCAA
AATGTTATTGAAAAATCAATCGTTGAAATGTTGCATTGGTTTGCAGGATCACAAGTTCGG
AATGTTGCTTCAATTGGTGGAAATATCGTTACAAGCTCACCAATATCTGATTTAAATCCA
ATTTTACTTGCTGCAGGTGCTAAATTAGAAGTTCAAAGTCTAAAAGATGGCAAAAGAATA
ATAAAAATGGATGAAAATTTCTTCACTGGATATCGTAAGAATTTAATCAAAGACAATGAA
ATTTTGGTTTCAATTTTGATTCCAAATACAAATAAAAATCAACATTTTGTGGCTTATAAG
CAAGCAAAAAGACGTGAAGATGATATTGCAATTGTCACTGCAGCTTTTAATTTCACCTTT
AAAAGCAACACAAATATCATTGAAGATGCAAAAATTGCTTTTGGTGGAATGGCTCAAACA
ACAATTTTAGCAATTAAAACAGCATCATTGATGAAAGGAAAAGAATGGAATCGAAAATTG
ATTGAAATTGTCAACCAAAGTTTAATTGATGAAATTCCATTGTCATTTGATGCACCAGGT
GGAAATGTTGTTTATCGTCGATCTTTGACTTTGAGTTTATTCTTCAAAGCATTTTTGAGC
ATCAGTCAAGAACTTGATAAATCATTGAATTTAAATATTTTAACTGATCGTGATCGAAGT
GGAATTGAAAGTTACCAAAATCTCACACCAAAGAGTTCACAATTATTTGAAAATGTCTCA
AGTGATCAACCTCTGACTGATCCAGTTCATCGTCCCAAAATTCATTCATCAGCGTTGCAA
CAAGCAACAGGAGAAGCAATTTATTGTGATGACATTCCAAAACATGAAAATGAACTTTAC
CTTTCACTTGTGTTGAGCACAAAAGCTCATGCTAAAATAATTTCAATTGATGCAAGTGAA
GCTCTTAAACAACCTGGAATTCATGCTTTTTACAGTGCTAAAGATTTAACAAAAGATCAA
AATTATTTCATGAATGAAGAACTTTTTACAAGTGAAATTGCAACAAATCAAGGCCGAATT
TTAGGAGCAATTGTTGGTGATAATCAAATCAAAGCTCAAAGGGCAGCAAAATTAGTAAAA
GTTGAATATGAAGATTTAAAACCAGTGATTGTCACACTTGAAGATGCAATCAAACAAAAA
TCTTATCATGAAAATTCACCAACGATTCTCGTCAATTGTGAAATTGAATCAGAATTTCAA
AAAGCTGAAAATATTTTTGAAGGAAAAGTTCGTTTAGGTGGACAAGAACATTTTTATTTA
GAAACTCAAGTTGCTCTTGCTATTCCAAAAGATTCTGATGAGCTTGAAATTTTTTCTTCA
ACACAAGAACCAGCAGTTCTACAAAATAATGCAGCAAAACTTTTACGACTAGCTGCTAAT
AAAATTGTTTGTAGAACTAAACGATTGGGTGGAGGTTTTGGTGGAAAACAAAGCAGAGCA
TCATTAGCAGCTCTTCCTGTAGCTTTCGCTGCTTATAAATTAAAACGACCAGTAAGAATA
ATGTTTGATAGAGATGAAGACATGATGATAACAGGTGGAAGAAATCCATTTTTATTTGAA
TACAAAATTTCATTTACAAATGAAGGAAAAATGACAGCACTTGAAGTTAAAGCTTATGTC
AATGCTGGATATTCACTTGAATCTTCGGACCTTGTTGTTTATAAAGCATCAAGTCACATT
ACTAATGCTTATAATATTCCTAAAGTTCGATTTGAAAGTCATGTTATGAAAACAAACACA
CCATCAAATAACGCATTCAGAGGTTTTGGAATTCCAGAAGCTCAAATGGTCAGCGAACAC
ATAATTCGTGAAATAGCAAATATTTTAAAGAAAGACTACATTGAAATTATGAAAATTAAC
TTGTTCAAAACAGGGGATGTAATTTTTTATAGACAATTGCTTGATGATTGCCATTCTATT
CGTTGTTTCCATGAAATTATCCAAACATCAAATTTCAAAGAAAGAAGAGCAAATGTTGAA
AAATTCAATTCTGAAAATCGATGGAAGAAGCGTGGAATAAGTTTGACAAATGTCATGTGT
GGTGTTGCTTATGGAGCACAATTTTTAAATCAAGCTGGAGTTCTGTTACATGTTTATCTT
GAAGGATCAGTTTTAGTTTCACATGGAGCAGTCGAAATGGGTCAAGGATTAAATATTAAA
ATTTTACAAATTGTCTCAACAACTCTCAAACTTCCGTTAGAAAGAATTCACATTCAAGAA
ACAGCAACTGACAAAGTTCCTAATGCACCGACAACAGGAGCATCAGTTGGTTCAGATATT
TATGGTGGAGCAGTTATTGAAGCTTGTCAAATAATTTTGAAAAGATTAGCACCATATAAA
GAGAAAATGCCAAATGCATCTTGGGATGATTGGATTAAAGTTGCATATTTCGATCGAGTT
TCACTTTCTACGACTGGCTTCTATGCAACTCCAGACATTGGACCAGAAATTAATAAGCCA
AGAAATTATTTCACTCATGGTTCAGCAGTTTCTGAAGTTGAAATTGATTGTTTGACTGGC
GATCATCAAGTGAATAAGAACTGA
>g9324.t1 Gene=g9324 Length=1167
MNTENEKNLVFFVNGKKITENEPDPEITLLRYLREKLKLTGTKLGCSEGGCGACTVMISK
FNRETNKVQHFSANACLMPVCALHGLAVTTVEGIGSTRDRLHPVQERIAKAHGSQCGFCT
PGMVMSMYALLRNSSKPSMKELEIAMQGNLCRCTGYRPIIEGYRTFTKEFGNEEVCGMGE
KCCKVNGGKLVDDKLFEVSEFVPYNPSQEPIFPPELKLNDQFDKETLKFINDRDVMWFRP
IELKELLKFKQEHGTAAKIVVGNTEVGVEVKFKNFDYKFLANPSQIRELNELEVTKDGLK
IGAAVTLTEIENFIESKTDQNVIEKSIVEMLHWFAGSQVRNVASIGGNIVTSSPISDLNP
ILLAAGAKLEVQSLKDGKRIIKMDENFFTGYRKNLIKDNEILVSILIPNTNKNQHFVAYK
QAKRREDDIAIVTAAFNFTFKSNTNIIEDAKIAFGGMAQTTILAIKTASLMKGKEWNRKL
IEIVNQSLIDEIPLSFDAPGGNVVYRRSLTLSLFFKAFLSISQELDKSLNLNILTDRDRS
GIESYQNLTPKSSQLFENVSSDQPLTDPVHRPKIHSSALQQATGEAIYCDDIPKHENELY
LSLVLSTKAHAKIISIDASEALKQPGIHAFYSAKDLTKDQNYFMNEELFTSEIATNQGRI
LGAIVGDNQIKAQRAAKLVKVEYEDLKPVIVTLEDAIKQKSYHENSPTILVNCEIESEFQ
KAENIFEGKVRLGGQEHFYLETQVALAIPKDSDELEIFSSTQEPAVLQNNAAKLLRLAAN
KIVCRTKRLGGGFGGKQSRASLAALPVAFAAYKLKRPVRIMFDRDEDMMITGGRNPFLFE
YKISFTNEGKMTALEVKAYVNAGYSLESSDLVVYKASSHITNAYNIPKVRFESHVMKTNT
PSNNAFRGFGIPEAQMVSEHIIREIANILKKDYIEIMKINLFKTGDVIFYRQLLDDCHSI
RCFHEIIQTSNFKERRANVEKFNSENRWKKRGISLTNVMCGVAYGAQFLNQAGVLLHVYL
EGSVLVSHGAVEMGQGLNIKILQIVSTTLKLPLERIHIQETATDKVPNAPTTGASVGSDI
YGGAVIEACQIILKRLAPYKEKMPNASWDDWIKVAYFDRVSLSTTGFYATPDIGPEINKP
RNYFTHGSAVSEVEIDCLTGDHQVNKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 17 | g9324.t1 | CDD | cd00207 | fer2 | 9 | 89 | 2.89727E-7 |
| 15 | g9324.t1 | Gene3D | G3DSA:3.30.365.10 | Aldehyde Oxidoreductase; domain 4 | 5 | 1167 | 0.0 |
| 7 | g9324.t1 | PANTHER | PTHR11908 | XANTHINE DEHYDROGENASE | 6 | 1163 | 0.0 |
| 8 | g9324.t1 | PANTHER | PTHR11908:SF86 | ALDEHYDE OXIDASE | 6 | 1163 | 0.0 |
| 16 | g9324.t1 | PIRSF | PIRSF000127 | Xanthine_dh | 1 | 1167 | 0.0 |
| 3 | g9324.t1 | Pfam | PF00111 | 2Fe-2S iron-sulfur cluster binding domain | 12 | 80 | 4.3E-10 |
| 5 | g9324.t1 | Pfam | PF01799 | [2Fe-2S] binding domain | 90 | 162 | 2.0E-30 |
| 1 | g9324.t1 | Pfam | PF00941 | FAD binding domain in molybdopterin dehydrogenase | 235 | 409 | 5.0E-47 |
| 4 | g9324.t1 | Pfam | PF03450 | CO dehydrogenase flavoprotein C-terminal domain | 418 | 520 | 2.4E-29 |
| 6 | g9324.t1 | Pfam | PF01315 | Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain | 583 | 687 | 1.6E-29 |
| 2 | g9324.t1 | Pfam | PF02738 | Molybdopterin-binding domain of aldehyde dehydrogenase | 713 | 1166 | 5.5E-143 |
| 18 | g9324.t1 | ProSitePatterns | PS00197 | 2Fe-2S ferredoxin-type iron-sulfur binding region signature. | 46 | 54 | - |
| 23 | g9324.t1 | ProSiteProfiles | PS51085 | 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. | 7 | 94 | 10.092 |
| 22 | g9324.t1 | ProSiteProfiles | PS51387 | PCMH-type FAD-binding domain profile. | 230 | 412 | 21.503 |
| 19 | g9324.t1 | SMART | SM01092 | CO_deh_flav_C_2 | 417 | 521 | 4.3E-26 |
| 20 | g9324.t1 | SMART | SM01008 | Ald_Xan_dh_C_2 | 583 | 687 | 3.2E-32 |
| 14 | g9324.t1 | SUPERFAMILY | SSF54292 | 2Fe-2S ferredoxin-like | 8 | 94 | 1.85E-22 |
| 10 | g9324.t1 | SUPERFAMILY | SSF47741 | CO dehydrogenase ISP C-domain like | 102 | 214 | 2.49E-35 |
| 13 | g9324.t1 | SUPERFAMILY | SSF56176 | FAD-binding/transporter-associated domain-like | 193 | 409 | 2.06E-62 |
| 9 | g9324.t1 | SUPERFAMILY | SSF55447 | CO dehydrogenase flavoprotein C-terminal domain-like | 413 | 526 | 5.36E-35 |
| 12 | g9324.t1 | SUPERFAMILY | SSF54665 | CO dehydrogenase molybdoprotein N-domain-like | 543 | 688 | 1.07E-35 |
| 11 | g9324.t1 | SUPERFAMILY | SSF56003 | Molybdenum cofactor-binding domain | 688 | 1165 | 7.85E-133 |
| 21 | g9324.t1 | TIGRFAM | TIGR02963 | xanthine_xdhA: xanthine dehydrogenase, small subunit | 9 | 520 | 4.5E-164 |
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:0005506 | iron ion 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 K00087 (xanthine dehydrogenase molybdenum-binding subunit)
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.
