Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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_3 g567 g567.t8 TSS g567.t8 4167939 4167939
chr_3 g567 g567.t8 isoform g567.t8 4168784 4170090
chr_3 g567 g567.t8 exon g567.t8.exon1 4168784 4169710
chr_3 g567 g567.t8 cds g567.t8.CDS1 4168969 4169710
chr_3 g567 g567.t8 exon g567.t8.exon2 4169872 4170090
chr_3 g567 g567.t8 cds g567.t8.CDS2 4169872 4169873
chr_3 g567 g567.t8 TTS g567.t8 NA NA

Sequences

>g567.t8 Gene=g567 Length=1146
GATACGACAGCACTTCAAAATTATTTTGGAATGACGGTCAAATAAGATTCAGTTTCATTG
GCGAAAAGTGTAATAAACTTGAAAACTATACTTTAAATGTGATACTTCAATGCGATTATG
CTGAAACGAAAAATGATTTTCTTGGCGTGTTTCATGATGATAGCGAATGTGAAGTTACAA
TACTTATGCGAACGCCAAAGGCGTGTTTAGAAATTCCTGAAAATGTCAAAAATGCAAAGA
TGTACGTAACTAGTCCCAATGGCAAGATTTTGAATTTCAACGCTTTAAAAAGTTCAAACC
ATATTATCAATGGTCCAAATGATGGAACTTTCATAATTGGTTTTCCAATTACTTACGAAC
ATGGAATTTTATGTGAAGCTGGCTCATCTATTTGTTATGTCGACAAGAATGAGACTGATT
TATCAAAGAAATATACCAATATGGGAACGATGACATCTAATATTGAATTTGAAAATGATC
GACCAGTCATTAAATTTACAAGCAAAGAAAAATGCAATAATAACACATTGGGCTCATCAA
AAATTGTTTTCGAATGTGATCGATTCAAAAAAGAAGGTACACCTAAATTTAAAGGTGTAA
AAGATTGTGTAAGCAATTTTGTTTGGGAAACATCACTTGCATGTTACGATGAAAAACCTT
GTGTTGTATCTGGAGAAAATGGTGATCAATACGATTTTAGTTCACTCGCAAATGTTCAAT
ATGAAGTTAAAATTCCAAACAAGACTGATGAAACCATTTACTTTTCTATTTGCTCAAATT
CAAAAGAATGTGGTGAAGGCAACTGGGGTAGTTGCATTGTAAAAAATACAGGTGGCAATA
AACAAACAACAAAAGTAGGCATCTTCAATGCAAAACTTCAAGTCGAGAAGAAAAATGTAT
TTTTGAAATATGATGAAGGTTCTCAATAAAAATTTAGATGATGAAGAAATAGACTTGAGG
CCATTAATCGACTATAATGGAAATTATTTGGCAAGAGTAAATGAAACAACCTTGCCAAAT
GAAACGTCAAAAAATAATGTGTCCTACTTGTTGAATGTATGTCGCCCGATAAATTCATTT
TATTCATTAAATTGTCATGGAAATACTGGCGCTTGTAGAACAATCATGAAAGATGAAAAA
CACGAA

>g567.t8 Gene=g567 Length=247
MRTPKACLEIPENVKNAKMYVTSPNGKILNFNALKSSNHIINGPNDGTFIIGFPITYEHG
ILCEAGSSICYVDKNETDLSKKYTNMGTMTSNIEFENDRPVIKFTSKEKCNNNTLGSSKI
VFECDRFKKEGTPKFKGVKDCVSNFVWETSLACYDEKPCVVSGENGDQYDFSSLANVQYE
VKIPNKTDETIYFSICSNSKECGEGNWGSCIVKNTGGNKQTTKVGIFNAKLQVEKKNVFL
KYDEGSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g567.t8 Gene3D G3DSA:2.70.130.10 - 19 155 0
8 g567.t8 Gene3D G3DSA:2.70.130.10 - 156 247 0
2 g567.t8 PANTHER PTHR15071 MANNOSE-6-PHOSPHATE RECEPTOR FAMILY MEMBER 69 246 0
3 g567.t8 PANTHER PTHR15071:SF17 CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR 69 246 0
1 g567.t8 Pfam PF00878 Cation-independent mannose-6-phosphate receptor repeat 118 246 0
6 g567.t8 SMART SM01404 CIMR_2 113 246 0
5 g567.t8 SUPERFAMILY SSF50911 Mannose 6-phosphate receptor domain 18 153 0
4 g567.t8 SUPERFAMILY SSF50911 Mannose 6-phosphate receptor domain 158 246 0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g567/g567.t8; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t8.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0038023 signaling receptor activity MF
GO:0007041 lysosomal transport BP
GO:0005537 mannose binding 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