General information for g567.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Cation-independent mannose-6-phosphate receptor.
Parent gene
- The parent gene g567 is located on chr_3: 4170778..4171803 (+ 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_3 | g567 | g567.t6 | TSS | g567.t6 | 4167939 | 4167939 |
| chr_3 | g567 | g567.t6 | isoform | g567.t6 | 4168099 | 4171502 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon1 | 4168099 | 4168164 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon2 | 4168457 | 4168676 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon3 | 4168784 | 4168850 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon4 | 4168915 | 4170520 |
| chr_3 | g567 | g567.t6 | cds | g567.t6.CDS1 | 4169023 | 4170520 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon5 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t6 | cds | g567.t6.CDS2 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon6 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t6 | cds | g567.t6.CDS3 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t6 | exon | g567.t6.exon7 | 4171422 | 4171502 |
| chr_3 | g567 | g567.t6 | cds | g567.t6.CDS4 | 4171422 | 4171502 |
| chr_3 | g567 | g567.t6 | TTS | g567.t6 | 4171812 | 4171812 |
Sequences
>g567.t6 Gene=g567 Length=2408
ATGAAGTATTTCGCAATTTTCCTGCTTGTGATAAATTTCTGCAATATAATTGCAATAGAT
CAAACAAAAGACGTTGAAGGAGCAAATTGTTCAGTGACAGAGACAATTGGAAATTATACA
TTTAATTTTACTGAACTTAGTAGTGACTTTGGATATCACATCGATGGAAATGCAGAAGAT
ATGGGAAAATATAGTTTCAATCTTTGTAAACCGCTATCAAGAAAATGCAACAACCAAACA
GCTGCAGCTTGTCTGAAAAATGTTGACGGCAAGGAAATCATAATAGGATACGACAGCACT
TCAAAATTATTTTGGAATGACGGTCAAATAAGATTCAGTTTCATTGGCGAAAAAATGATT
TTCTTGGCGTGTTTCATGATGATAGCGAATGTGAAGTTACAATACTTATGCGAACGCCAA
AGGCGTGTTTAGAAATTCCTGAAAATGTCAAAAATGCAAAGATGTACGTAACTAGTCCCA
ATGGCAAGATTTTGAATTTCAACGCTTTAAAAAGTTCAAACCATATTATCAATGGTCCAA
ATGATGGAACTTTCATAATTGGTTTTCCAATTACTTACGAACATGGAATTTTATGTGAAG
CTGGCTCATCTATTTGTTATGTCGACAAGAATGAGACTGATTTATCAAAGAAATATACCA
ATATGGGAACGATGACATCTAATATTGAATTTGAAAATGATCGACCAGTCATTAAATTTA
CAAGCAAAGAAAAATGCAATAATAACACATTGGGCTCATCAAAAATTGTTTTCGAATGTG
ATCGATTCAAAAAAGAAGGTACACCTAAATTTAAAGGTGTAAAAGATTGTGTAAGCAATT
TTGTTTGGGAAACATCACTTGCATGTTACGATGAAAAACCTTGTGTTGTATCTGGAGAAA
ATGGTGATCAATACGATTTTAGTTCACTCGCAAATGTTCAATATGAAGTTAAAATTCCAA
ACAAGACTGATGAAACCATTTACTTTTCTATTTGCTCAAATTCAAAAGAATGTGGTGAAG
GCAACTGGGGTAGTTGCATTGTAAAAAATACAGGTGGCAATAAACAAACAACAAAAGTAG
GCATCTTCAATGCAAAACTTCAAGTCGAGAAGAAAAATGTATTTTTGAAATATGATGAAG
GTTCTCAATGTGGTGATCCGAAAGATAAGAAAAAATATTCAACAAGAATCGAATTTAATG
TTGCTGATAGCCCAAATGATGAAGAAATTGTATTAATTGAGGATAAATGTGAAATTGTCA
TTCACTTCAAGACACTCTTGGCTAATCAACATGTAAAGAATTGCGTCGTTAAAAATTTAG
ATGATGAAGAAATAGACTTGAGGCCATTAATCGACTATAATGGAAATTATTTGGCAAGAG
TAAATGAAACAACCTTGCCAAATGAAACGTCAAAAAATAATGTGTCCTACTTGTTGAATG
TATGTCGCCCGATAAATTCATTTTATTCATTAAATTGTCATGGAAATACTGGCGCTTGTA
GAACAATCATGAAAGATGAAAAACACGAAGAGGAAATAAGCTTAGGTCACTTTGAATATT
TTATGTCTACTGAAAAGGGAAAAATTGAAGGTACAAACAATGTTATAATGAAATATTTCC
ATGGATCAAAATGTCCAACTGATAAAGAGGAAGAGATAACAACGAAAGTTAAATTCTATT
GTGATGAGAATGCTGGTTTGGGAAGTCCTATTTTACAATCTATTGAGCATTGTGAATATT
CATTTGAATTTCCAACCAGCATCTTATGCAATGATAAGCGTGTCAATCTGAAAAGCAATG
AATCGTGCATACTGACGAATGGTGATTCGAGTGTCAATTTGAAATCTTATGGAAATTTCA
ATACAAGCAACAGAAACATAAGTTTGTGTGATGCACTTGTGAAGACATACACTATCAGCT
ATAAACAATCAATGGTTATTATTGAATATGTTGATAAAGATTACGTCGATATAGAAGTTC
AACTTAAATGTAATTTGAAAAATAATACATTTGTTGATGTTAGCAATGAGGGTATCATCA
TTATGAATGAGTCACCTTTGATTTGTCCACTTTTGCATATCGTACCAAAAGCTACACCAT
CACAGAATGAAGTTGATAACGATAACAATGATGTGCTAGAGATGTCATTAAACAATGATA
TAATAATACCAAAATCAAGCAAATTTCCATTGGGTTATTTGTTCCTAATTTCAATTTTGA
TTGCTGCATTTGGAATTTTCTATATTGTCATAAGAAATCCTGAGCGTCGCGACATAATTC
GCAATATGATTAAATTCCGATCTCGGTCAAATGTTCGATACACACGAGTGCGACTTAATG
AAGAATCAGCCCTCTTAGATGGTAATAGTCCAAATTCAGATAGTGATGATGAGAATATTT
TGCTGTAA
>g567.t6 Gene=g567 Length=648
MYVTSPNGKILNFNALKSSNHIINGPNDGTFIIGFPITYEHGILCEAGSSICYVDKNETD
LSKKYTNMGTMTSNIEFENDRPVIKFTSKEKCNNNTLGSSKIVFECDRFKKEGTPKFKGV
KDCVSNFVWETSLACYDEKPCVVSGENGDQYDFSSLANVQYEVKIPNKTDETIYFSICSN
SKECGEGNWGSCIVKNTGGNKQTTKVGIFNAKLQVEKKNVFLKYDEGSQCGDPKDKKKYS
TRIEFNVADSPNDEEIVLIEDKCEIVIHFKTLLANQHVKNCVVKNLDDEEIDLRPLIDYN
GNYLARVNETTLPNETSKNNVSYLLNVCRPINSFYSLNCHGNTGACRTIMKDEKHEEEIS
LGHFEYFMSTEKGKIEGTNNVIMKYFHGSKCPTDKEEEITTKVKFYCDENAGLGSPILQS
IEHCEYSFEFPTSILCNDKRVNLKSNESCILTNGDSSVNLKSYGNFNTSNRNISLCDALV
KTYTISYKQSMVIIEYVDKDYVDIEVQLKCNLKNNTFVDVSNEGIIIMNESPLICPLLHI
VPKATPSQNEVDNDNNDVLEMSLNNDIIIPKSSKFPLGYLFLISILIAAFGIFYIVIRNP
ERRDIIRNMIKFRSRSNVRYTRVRLNEESALLDGNSPNSDSDDENILL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g567.t6 | Gene3D | G3DSA:2.70.130.10 | - | 2 | 138 | 2.3E-18 |
| 15 | g567.t6 | Gene3D | G3DSA:2.70.130.10 | - | 139 | 279 | 5.4E-20 |
| 14 | g567.t6 | Gene3D | G3DSA:2.70.130.10 | - | 280 | 440 | 8.0E-29 |
| 3 | g567.t6 | PANTHER | PTHR15071 | MANNOSE-6-PHOSPHATE RECEPTOR FAMILY MEMBER | 54 | 246 | 1.9E-43 |
| 5 | g567.t6 | PANTHER | PTHR15071:SF17 | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | 54 | 246 | 1.9E-43 |
| 4 | g567.t6 | PANTHER | PTHR15071 | MANNOSE-6-PHOSPHATE RECEPTOR FAMILY MEMBER | 166 | 454 | 1.9E-43 |
| 6 | g567.t6 | PANTHER | PTHR15071:SF17 | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | 166 | 454 | 1.9E-43 |
| 2 | g567.t6 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 100 | 231 | 1.8E-17 |
| 1 | g567.t6 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 238 | 391 | 4.3E-10 |
| 17 | g567.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 576 | - |
| 18 | g567.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 577 | 597 | - |
| 16 | g567.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 598 | 648 | - |
| 12 | g567.t6 | SMART | SM01404 | CIMR_2 | 95 | 231 | 8.3E-24 |
| 11 | g567.t6 | SMART | SM01404 | CIMR_2 | 236 | 392 | 1.1E-14 |
| 9 | g567.t6 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 2 | 135 | 2.09E-16 |
| 8 | g567.t6 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 140 | 273 | 9.94E-15 |
| 10 | g567.t6 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 262 | 436 | 3.92E-23 |
| 7 | g567.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 575 | 597 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g567/g567.t6; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t6.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.
