Gene loci information

Transcript annotation

  • This transcript has been annotated as Xanthine dehydrogenase.

Parent gene

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 g9323 g9323.t1 isoform g9323.t1 1855289 1858864
chr_1 g9323 g9323.t1 exon g9323.t1.exon1 1855289 1855418
chr_1 g9323 g9323.t1 cds g9323.t1.CDS1 1855289 1855418
chr_1 g9323 g9323.t1 exon g9323.t1.exon2 1855706 1856069
chr_1 g9323 g9323.t1 cds g9323.t1.CDS2 1855706 1856069
chr_1 g9323 g9323.t1 exon g9323.t1.exon3 1856122 1856699
chr_1 g9323 g9323.t1 cds g9323.t1.CDS3 1856122 1856699
chr_1 g9323 g9323.t1 exon g9323.t1.exon4 1857171 1857470
chr_1 g9323 g9323.t1 cds g9323.t1.CDS4 1857171 1857470
chr_1 g9323 g9323.t1 exon g9323.t1.exon5 1857525 1858753
chr_1 g9323 g9323.t1 cds g9323.t1.CDS5 1857525 1858753
chr_1 g9323 g9323.t1 exon g9323.t1.exon6 1858814 1858864
chr_1 g9323 g9323.t1 cds g9323.t1.CDS6 1858814 1858864
chr_1 g9323 g9323.t1 TTS g9323.t1 1858953 1858953
chr_1 g9323 g9323.t1 TSS g9323.t1 NA NA

Sequences

>g9323.t1 Gene=g9323 Length=2652
ATGTTGCATTGGTTTTCTGGTACTCAAGTTCGTAATGTAGCTTCAATTGGTGGAAATATC
GTTACAAGCTCACCAATATCTGATTTAAATCCAATTTTACTTGCTGCAGGTGCTAAATTA
GAAGTTCAAACATCATTGATGAAAGGAAAAGAATGGAATCGAAAATTGATTGAAATTGTC
AACCAAAGTTTAATTGATGAAATTCCATTGTCATTTGATGCACCAGGTGGAAATGTTGTT
TATCGTCGATCTTTGACTTTGAGTTTATTCTTCAAAGCATTTTTGAGCATCAGTCAAGAA
CTTGATAAATCATTGAATTTAAATATTTTAACTGATCGTGATCGAAGTGGAATTGAAAGT
TACCAAAATCTCACACCAAAGAGTTCACAATTATTTGAAAATGTCTCAAGTGATCAACCT
CTGACTGATCCAGTTCTCGTCCCAAAATTCATTCATCAGCGTTGCAACAAGCAACAGGAA
GAAAGCAATTTATTCACAAAAGCTCATGCTAAAATAATTTCGATTGATGCAAGTGAAGCT
CTTAAACAACCTGGAATTCATGCCTTCTTTACAGCAAAAGACGTTGATCAATCAAGATTT
ATCAATGGACTTTTAGCAAAAGATGAAGAAATATTCATTAGTGAAACTGTCACAAGTGAA
GGTCAAATTTTAGGAGCAATTGTTGGTGACAATCAAATTATAGCTCAAAGAGCAGCAAAA
TTGGTGAAAGTTGAATATGAAGAATTAAGTCCAGTCATAATAACTCTTGAAGATGCAATT
AAGCAAAATTCATATTTTCCTGGTTTTCCTCATGTCGTTTCAAACGGAAATATTGAGAAA
ATTTTAAATGAAGCAGATCATGTAATTAAAGGAGAAGTTCGTTTAGGTGGTCAAGAACAT
TTTTACATTGAAACTCATTCAAATCTTGCAATTCCTAAAGATGCAGATGAAATTGAAATT
TTTTCATCAACTCAACAACCTGGCGAAGTTCAACGTCATGTTGCTAATTTTTTGAACATT
CCACAAAACAAAGTTGTATGTCGTACTAAAAGAATTGGCGGCGGTTTTGGAGGTAAGGAG
ACGAGAGGTTCTTTGGCTACATTGCCAGTTGCTTTTGCTGCTTACAAATTGAAACGACCA
GTGCGAATGATTTTAGACAGAGATGAAGATATGATGATAACAGGAGGAAGAAATCCAATG
TTATTTAAATACAAAATTGCTTGCACAAAAGAGGGAAAAATTTTGGGTTGCGATGTTCGA
GCTTTTATTAATGCTGGTTATTCATTGGATTATTCTCATTATGTCATCGAAAGTGCATAT
TCTTCAATTGCAAATTGTTATAAATTCAATGTTGTCAATTATGAATTCAATGTTCTAAAA
ACAAACACCAGATCGAACACAGCTTTTAGAGGTTTTGGATCACCTCAAGGAATGTTGGCA
GCTGAGACAATAATCAGAGATGTTGCACGAATTACAGGCAAAGATTATCTTGAAATTATG
GACCTAAATATGTGTGAAAATGGCTATGTTCTGCATTATAAACAAATACTTGAAAACTGC
AATATCAGAAGATGCTTTGAAGAAGTAAAAATTAATTCTGATTTAGAAAACAGACGAAAA
TCTGTTGCAAAATTCAACTCTGAAAATCGATGGAAGAAGCGAGGAATTTCGATCGTTAAC
AATCTTTTCGGTATAGGATTTCCTCCTAAGTTCATGAACCAAGGTGGTGCACTTGTCCAT
ATTTATCTTGATGGTTCAGTTTTGGTCTCTCATGGTGGAGTCGAAATGGGTCAAGGACTG
CATACTAAGATGATTCAAGTAGCATCACGAGTATTGAATGTTCCGATGGAAATTATTCAC
ATTCAAGAAACAGCAACTGACAAAGTTCCTAATGCCACTAGCACAGCAGCTTCTGTAAGT
TCCGATTTATATGGTGGAGCAGTTATGAATGCTTGTGAAATTTTGAATGAACGTCTTGCA
CCATATAAAAAGAAAATGCCAAATGCATCTTGGGATGATTGGATTAAAGTTGCATATTTC
GATCGAGTTTCACTTTCTACGACTGGCTTTTATGCAACTCCAGACATTGGACCAGAAATT
AATAAACCTAAAAATTATTTCACTCATGGTTCTGCAGTTTCTGAAGTTGAAATTGATTGT
TTGACTGGCGATCATCAAGTGATAAGAACTGACATTGTGATGGATGTTGGAAGCTCATTG
AATCCAGCAATTGACATTGGTCAAATTGAAGGTGCTTTCATGCAAGGTTATGGATTATTT
GTGCTTGAAGAATTGATTTATTCGCCAAATGGAACTTTGTATTCACGAGGTCCAGGCATG
TACAAAATTCCAAGTTTCGGCAACATTCCAGCTGAATTCAATGTTTCACTGCTCACTGAT
GCACCAAATCCGAGAGCTGTGTTTTCATCTCGAGCTGTTGGTGAACCACCATTATTTTTA
GCATCATCAGTTTATTTTGCAATTAAAGAAGCGATTGGAGCAGCAAGAAAAGAAGAAGGC
TTGGATTCACACTTTTATTTACAAGCACCAGCAACAGCAGCAAGAATTAGAGTCGCATGT
CAAGATAAAATTGTTGAAAAGTTTGAGACATTAAAAAATGAAAGTTTGACACCATGGAAC
GTTGATTTATAA

>g9323.t1 Gene=g9323 Length=883
MLHWFSGTQVRNVASIGGNIVTSSPISDLNPILLAAGAKLEVQTSLMKGKEWNRKLIEIV
NQSLIDEIPLSFDAPGGNVVYRRSLTLSLFFKAFLSISQELDKSLNLNILTDRDRSGIES
YQNLTPKSSQLFENVSSDQPLTDPVLVPKFIHQRCNKQQEESNLFTKAHAKIISIDASEA
LKQPGIHAFFTAKDVDQSRFINGLLAKDEEIFISETVTSEGQILGAIVGDNQIIAQRAAK
LVKVEYEELSPVIITLEDAIKQNSYFPGFPHVVSNGNIEKILNEADHVIKGEVRLGGQEH
FYIETHSNLAIPKDADEIEIFSSTQQPGEVQRHVANFLNIPQNKVVCRTKRIGGGFGGKE
TRGSLATLPVAFAAYKLKRPVRMILDRDEDMMITGGRNPMLFKYKIACTKEGKILGCDVR
AFINAGYSLDYSHYVIESAYSSIANCYKFNVVNYEFNVLKTNTRSNTAFRGFGSPQGMLA
AETIIRDVARITGKDYLEIMDLNMCENGYVLHYKQILENCNIRRCFEEVKINSDLENRRK
SVAKFNSENRWKKRGISIVNNLFGIGFPPKFMNQGGALVHIYLDGSVLVSHGGVEMGQGL
HTKMIQVASRVLNVPMEIIHIQETATDKVPNATSTAASVSSDLYGGAVMNACEILNERLA
PYKKKMPNASWDDWIKVAYFDRVSLSTTGFYATPDIGPEINKPKNYFTHGSAVSEVEIDC
LTGDHQVIRTDIVMDVGSSLNPAIDIGQIEGAFMQGYGLFVLEELIYSPNGTLYSRGPGM
YKIPSFGNIPAEFNVSLLTDAPNPRAVFSSRAVGEPPLFLASSVYFAIKEAIGAARKEEG
LDSHFYLQAPATAARIRVACQDKIVEKFETLKNESLTPWNVDL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 1 44 0.0000000
14 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 45 158 0.0000000
18 g9323.t1 Gene3D G3DSA:3.90.1170.50 - 166 251 0.0000000
17 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 252 517 0.0000000
15 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 300 394 0.0000000
16 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 518 864 0.0000000
13 g9323.t1 Gene3D G3DSA:3.30.365.10 Aldehyde Oxidoreductase; domain 4 569 696 0.0000000
5 g9323.t1 PANTHER PTHR11908 XANTHINE DEHYDROGENASE 1 867 0.0000000
6 g9323.t1 PANTHER PTHR11908:SF100 XANTHINE DEHYDROGENASE 1 867 0.0000000
1 g9323.t1 Pfam PF00941 FAD binding domain in molybdopterin dehydrogenase 2 44 0.0000000
3 g9323.t1 Pfam PF03450 CO dehydrogenase flavoprotein C-terminal domain 45 96 0.0000002
4 g9323.t1 Pfam PF01315 Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain 166 249 0.0000000
2 g9323.t1 Pfam PF02738 Molybdopterin-binding domain of aldehyde dehydrogenase 272 790 0.0000000
19 g9323.t1 ProSiteProfiles PS51387 PCMH-type FAD-binding domain profile. 1 92 9.3020000
11 g9323.t1 SMART SM01008 Ald_Xan_dh_C_2 166 250 0.0000000
10 g9323.t1 SUPERFAMILY SSF56176 FAD-binding/transporter-associated domain-like 1 44 0.0000000
7 g9323.t1 SUPERFAMILY SSF55447 CO dehydrogenase flavoprotein C-terminal domain-like 45 102 0.0000000
9 g9323.t1 SUPERFAMILY SSF54665 CO dehydrogenase molybdoprotein N-domain-like 166 266 0.0000000
8 g9323.t1 SUPERFAMILY SSF56003 Molybdenum cofactor-binding domain 251 866 0.0000000

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:0050660 flavin adenine dinucleotide binding MF
GO:0055114 NA NA
GO:0071949 FAD binding MF
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

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. There were no conditions that were differentially expressed