Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative oxidoreductase GLYR1-like protein.

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_2 g4450 g4450.t1 TSS g4450.t1 2440235 2440235
chr_2 g4450 g4450.t1 isoform g4450.t1 2440346 2442282
chr_2 g4450 g4450.t1 exon g4450.t1.exon1 2440346 2440395
chr_2 g4450 g4450.t1 cds g4450.t1.CDS1 2440346 2440395
chr_2 g4450 g4450.t1 exon g4450.t1.exon2 2440530 2440652
chr_2 g4450 g4450.t1 cds g4450.t1.CDS2 2440530 2440652
chr_2 g4450 g4450.t1 exon g4450.t1.exon3 2440710 2440859
chr_2 g4450 g4450.t1 cds g4450.t1.CDS3 2440710 2440859
chr_2 g4450 g4450.t1 exon g4450.t1.exon4 2440917 2442282
chr_2 g4450 g4450.t1 cds g4450.t1.CDS4 2440917 2442282
chr_2 g4450 g4450.t1 TTS g4450.t1 2442564 2442564

Sequences

>g4450.t1 Gene=g4450 Length=1689
ATGGCTGACAAGAATAAAGTGTATACTTATAAAATGCATGATCTCGTATGGGCTAAAATG
CCGAGTTATTGCTACTGGCCAGGACGTATAGTTGAACCAAACACTCCACAAATCGCAAAG
TTAAAAAAAAGTCCATCTCAGTTGTGCATTTTCTTTTTTGGATCTAATAATTATACTTGG
CTTGAAGAGAAAAATTTGAAACCATATTCAGAATTTCGTGAAGAATTTATGGCAAAAGGA
AAACCAAAAGATCAATTTATGGCAGCCATGAATGATATTGACTCTTTCATTGAAAATCCA
GATAATTTTTCAGCTTTATTTGAACCAAAAACACCGATTCAAAAGAAGAAAAACACTCCG
AAACCAAAGCAAAAACAAGATATCGAAGCTGATTTTGATAGTCTCAAGTCAGACTCTAGT
GTACCTTCGTCACCAAGTTTGAAACCTTCTCAATCGGCACTCTCAAACACAGTTTCATCT
CCAGTAATTACTGCACGTGCATCTGCAATTGATAAATCTTCCAAATCAGAAAAAGTGCCT
CAAAAGAAGCGCAAATCAACTCGTGAATCAGAACTTTTTGATGAAGATATGGATCTTGAA
GAACCTGTAATGTCACAACCACAATCAAAGAAATCAAGAAAGTCAAGCAATTTGGGCACA
TCACCACGAAATACTGAAACAGCGTATGAACCGCGTCGTCGTTCTGATATTGCTGAAGCT
ACAAAAACATTAAAATCTCCTCGTCGTGCAGAAACTTCTTCAAATGTCTATGGATTGATT
GGAGTTGGAATTATGGGAAGTAGCATCTTACAAAATTTACTCGCTAGCTCAAATGAAGTT
ATAATTTACAATCGTAATCCAGCTCGATGCGAAACGTTTGCCAATCAAAATTGCACAGTT
GTTGAAAGCCCACGTGAAGTTTTTGAGCAAGCGAACATTACGCTTATTTGTGTATCAGAT
TGTGATGCAGTGAAAGAAGTTGTGTGCCAAGGAGAAACTGGAATTTTGGCCGCAGATACA
AATTCATTAGATAAGGGTGTTATAATGCTTAGTTCAATTGACTGTGAAACATCTCGTGAC
ATTCAAACAGCTTTGTCTATGAAATCAATTCGTTATCTCGAAGCACAATTACAAGGGCCA
AAAGATGAAACGAAAGATAAACTAATTGTTATCACAGCTGGTGATAATTCATTATATCTG
GATAGTAAGAGCTGTTTGGAATCATTTGCTAAAGACACATATTATTTGGGAGACGATGTC
GAATCAGCAATTAAAATGAATTTAGTACTTCATTCGATTGCAGGTGTTCAATTGGCTGCA
TTGACAGAGGCACTTGCTTTAGCGGATTCACTTGGATTACAGTTACGCGATATTCTTGAA
ATTATTGAACTTAGCAACATCAATTCTGATTTTATCGTTGAGAAAGGAAAATATATTGTT
GATGAAAAATTCCGCGATCCATCAACAAAAATTGAGACAACTTCGAAAGATTTAAAAATG
GTCATTGAGCTTGGTGATTCTTTAGATCAACCATTACCACTTGTAGCTGCATCAAAAGAA
CTATTTAAAGTGGCAAAACGTATGGGTTTTGAAGAAAGTGATTCAAGTGCAGTCTACTTT
GCTTCAAATTTTAACAAATACATCTATGAGTTTGCGAATTATTCTGCCGCTGAGAATGGA
ACTATGTAA

>g4450.t1 Gene=g4450 Length=562
MADKNKVYTYKMHDLVWAKMPSYCYWPGRIVEPNTPQIAKLKKSPSQLCIFFFGSNNYTW
LEEKNLKPYSEFREEFMAKGKPKDQFMAAMNDIDSFIENPDNFSALFEPKTPIQKKKNTP
KPKQKQDIEADFDSLKSDSSVPSSPSLKPSQSALSNTVSSPVITARASAIDKSSKSEKVP
QKKRKSTRESELFDEDMDLEEPVMSQPQSKKSRKSSNLGTSPRNTETAYEPRRRSDIAEA
TKTLKSPRRAETSSNVYGLIGVGIMGSSILQNLLASSNEVIIYNRNPARCETFANQNCTV
VESPREVFEQANITLICVSDCDAVKEVVCQGETGILAADTNSLDKGVIMLSSIDCETSRD
IQTALSMKSIRYLEAQLQGPKDETKDKLIVITAGDNSLYLDSKSCLESFAKDTYYLGDDV
ESAIKMNLVLHSIAGVQLAALTEALALADSLGLQLRDILEIIELSNINSDFIVEKGKYIV
DEKFRDPSTKIETTSKDLKMVIELGDSLDQPLPLVAASKELFKVAKRMGFEESDSSAVYF
ASNFNKYIYEFANYSAAENGTM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g4450.t1 Gene3D G3DSA:2.30.30.140 - 3 102 4.7E-23
16 g4450.t1 Gene3D G3DSA:3.40.50.720 - 238 416 2.7E-30
18 g4450.t1 Gene3D G3DSA:1.10.1040.10 - 417 543 5.7E-23
10 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 108 249 -
15 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 120 134 -
13 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 136 170 -
11 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 171 192 -
14 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 205 226 -
12 g4450.t1 MobiDBLite mobidb-lite consensus disorder prediction 227 246 -
4 g4450.t1 PANTHER PTHR43580 OXIDOREDUCTASE GLYR1-RELATED 257 542 7.2E-73
5 g4450.t1 PANTHER PTHR43580:SF2 OXIDOREDUCTASE GLYR1-RELATED 257 542 7.2E-73
1 g4450.t1 Pfam PF00855 PWWP domain 10 94 1.8E-18
3 g4450.t1 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase 257 417 1.1E-22
2 g4450.t1 Pfam PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase 428 539 2.1E-16
19 g4450.t1 ProSiteProfiles PS50812 PWWP domain profile. 12 72 15.713
9 g4450.t1 SMART SM00293 PWWP_4 10 70 2.4E-12
6 g4450.t1 SUPERFAMILY SSF63748 Tudor/PWWP/MBT 9 99 5.05E-22
7 g4450.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 258 418 1.16E-22
8 g4450.t1 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 422 541 6.23E-18

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:0050661 NADP binding MF
GO:0051287 NAD binding MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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.

Raw TPM values