General information for g567.t1
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.t1 | TSS | g567.t1 | 4167939 | 4167939 |
| chr_3 | g567 | g567.t1 | isoform | g567.t1 | 4168099 | 4171502 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon1 | 4168099 | 4168164 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS1 | 4168099 | 4168164 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon2 | 4168457 | 4168676 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS2 | 4168457 | 4168676 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon3 | 4168784 | 4170520 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS3 | 4168784 | 4170520 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon4 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS4 | 4170581 | 4170648 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon5 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS5 | 4170710 | 4171009 |
| chr_3 | g567 | g567.t1 | exon | g567.t1.exon6 | 4171422 | 4171502 |
| chr_3 | g567 | g567.t1 | cds | g567.t1.CDS6 | 4171422 | 4171502 |
| chr_3 | g567 | g567.t1 | TTS | g567.t1 | 4171812 | 4171812 |
Sequences
>g567.t1 Gene=g567 Length=2472
ATGAAGTATTTCGCAATTTTCCTGCTTGTGATAAATTTCTGCAATATAATTGCAATAGAT
CAAACAAAAGACGTTGAAGGAGCAAATTGTTCAGTGACAGAGACAATTGGAAATTATACA
TTTAATTTTACTGAACTTAGTAGTGACTTTGGATATCACATCGATGGAAATGCAGAAGAT
ATGGGAAAATATAGTTTCAATCTTTGTAAACCGCTATCAAGAAAATGCAACAACCAAACA
GCTGCAGCTTGTCTGAAAAATGTTGACGGCAAGGAAATCATAATAGGATACGACAGCACT
TCAAAATTATTTTGGAATGACGGTCAAATAAGATTCAGTTTCATTGGCGAAAAGTGTAAT
AAACTTGAAAACTATACTTTAAATGTGATACTTCAATGCGATTATGCTGAAACGAAAAAT
GATTTTCTTGGCGTGTTTCATGATGATAGCGAATGTGAAGTTACAATACTTATGCGAACG
CCAAAGGCGTGTTTAGAAATTCCTGAAAATGTCAAAAATGCAAAGATGTACGTAACTAGT
CCCAATGGCAAGATTTTGAATTTCAACGCTTTAAAAAGTTCAAACCATATTATCAATGGT
CCAAATGATGGAACTTTCATAATTGGTTTTCCAATTACTTACGAACATGGAATTTTATGT
GAAGCTGGCTCATCTATTTGTTATGTCGACAAGAATGAGACTGATTTATCAAAGAAATAT
ACCAATATGGGAACGATGACATCTAATATTGAATTTGAAAATGATCGACCAGTCATTAAA
TTTACAAGCAAAGAAAAATGCAATAATAACACATTGGGCTCATCAAAAATTGTTTTCGAA
TGTGATCGATTCAAAAAAGAAGGTACACCTAAATTTAAAGGTGTAAAAGATTGTGTAAGC
AATTTTGTTTGGGAAACATCACTTGCATGTTACGATGAAAAACCTTGTGTTGTATCTGGA
GAAAATGGTGATCAATACGATTTTAGTTCACTCGCAAATGTTCAATATGAAGTTAAAATT
CCAAACAAGACTGATGAAACCATTTACTTTTCTATTTGCTCAAATTCAAAAGAATGTGGT
GAAGGCAACTGGGGTAGTTGCATTGTAAAAAATACAGGTGGCAATAAACAAACAACAAAA
GTAGGCATCTTCAATGCAAAACTTCAAGTCGAGAAGAAAAATGTATTTTTGAAATATGAT
GAAGGTTCTCAATGTGGTGATCCGAAAGATAAGAAAAAATATTCAACAAGAATCGAATTT
AATGTTGCTGATAGCCCAAATGATGAAGAAATTGTATTAATTGAGGATAAATGTGAAATT
GTCATTCACTTCAAGACACTCTTGGCTAATCAACATGTAAAGAATTGCGTCGTTAAAAAT
TTAGATGATGAAGAAATAGACTTGAGGCCATTAATCGACTATAATGGAAATTATTTGGCA
AGAGTAAATGAAACAACCTTGCCAAATGAAACGTCAAAAAATAATGTGTCCTACTTGTTG
AATGTATGTCGCCCGATAAATTCATTTTATTCATTAAATTGTCATGGAAATACTGGCGCT
TGTAGAACAATCATGAAAGATGAAAAACACGAAGAGGAAATAAGCTTAGGTCACTTTGAA
TATTTTATGTCTACTGAAAAGGGAAAAATTGAAGGTACAAACAATGTTATAATGAAATAT
TTCCATGGATCAAAATGTCCAACTGATAAAGAGGAAGAGATAACAACGAAAGTTAAATTC
TATTGTGATGAGAATGCTGGTTTGGGAAGTCCTATTTTACAATCTATTGAGCATTGTGAA
TATTCATTTGAATTTCCAACCAGCATCTTATGCAATGATAAGCGTGTCAATCTGAAAAGC
AATGAATCGTGCATACTGACGAATGGTGATTCGAGTGTCAATTTGAAATCTTATGGAAAT
TTCAATACAAGCAACAGAAACATAAGTTTGTGTGATGCACTTGTGAAGACATACACTATC
AGCTATAAACAATCAATGGTTATTATTGAATATGTTGATAAAGATTACGTCGATATAGAA
GTTCAACTTAAATGTAATTTGAAAAATAATACATTTGTTGATGTTAGCAATGAGGGTATC
ATCATTATGAATGAGTCACCTTTGATTTGTCCACTTTTGCATATCGTACCAAAAGCTACA
CCATCACAGAATGAAGTTGATAACGATAACAATGATGTGCTAGAGATGTCATTAAACAAT
GATATAATAATACCAAAATCAAGCAAATTTCCATTGGGTTATTTGTTCCTAATTTCAATT
TTGATTGCTGCATTTGGAATTTTCTATATTGTCATAAGAAATCCTGAGCGTCGCGACATA
ATTCGCAATATGATTAAATTCCGATCTCGGTCAAATGTTCGATACACACGAGTGCGACTT
AATGAAGAATCAGCCCTCTTAGATGGTAATAGTCCAAATTCAGATAGTGATGATGAGAAT
ATTTTGCTGTAA
>g567.t1 Gene=g567 Length=823
MKYFAIFLLVINFCNIIAIDQTKDVEGANCSVTETIGNYTFNFTELSSDFGYHIDGNAED
MGKYSFNLCKPLSRKCNNQTAAACLKNVDGKEIIIGYDSTSKLFWNDGQIRFSFIGEKCN
KLENYTLNVILQCDYAETKNDFLGVFHDDSECEVTILMRTPKACLEIPENVKNAKMYVTS
PNGKILNFNALKSSNHIINGPNDGTFIIGFPITYEHGILCEAGSSICYVDKNETDLSKKY
TNMGTMTSNIEFENDRPVIKFTSKEKCNNNTLGSSKIVFECDRFKKEGTPKFKGVKDCVS
NFVWETSLACYDEKPCVVSGENGDQYDFSSLANVQYEVKIPNKTDETIYFSICSNSKECG
EGNWGSCIVKNTGGNKQTTKVGIFNAKLQVEKKNVFLKYDEGSQCGDPKDKKKYSTRIEF
NVADSPNDEEIVLIEDKCEIVIHFKTLLANQHVKNCVVKNLDDEEIDLRPLIDYNGNYLA
RVNETTLPNETSKNNVSYLLNVCRPINSFYSLNCHGNTGACRTIMKDEKHEEEISLGHFE
YFMSTEKGKIEGTNNVIMKYFHGSKCPTDKEEEITTKVKFYCDENAGLGSPILQSIEHCE
YSFEFPTSILCNDKRVNLKSNESCILTNGDSSVNLKSYGNFNTSNRNISLCDALVKTYTI
SYKQSMVIIEYVDKDYVDIEVQLKCNLKNNTFVDVSNEGIIIMNESPLICPLLHIVPKAT
PSQNEVDNDNNDVLEMSLNNDIIIPKSSKFPLGYLFLISILIAAFGIFYIVIRNPERRDI
IRNMIKFRSRSNVRYTRVRLNEESALLDGNSPNSDSDDENILL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g567.t1 | Gene3D | G3DSA:2.70.130.10 | - | 23 | 175 | 3.9E-20 |
| 13 | g567.t1 | Gene3D | G3DSA:2.70.130.10 | - | 176 | 313 | 3.2E-18 |
| 12 | g567.t1 | Gene3D | G3DSA:2.70.130.10 | - | 314 | 453 | 8.1E-20 |
| 14 | g567.t1 | Gene3D | G3DSA:2.70.130.10 | - | 454 | 615 | 1.2E-28 |
| 4 | g567.t1 | PANTHER | PTHR15071 | MANNOSE-6-PHOSPHATE RECEPTOR FAMILY MEMBER | 29 | 421 | 2.8E-56 |
| 6 | g567.t1 | PANTHER | PTHR15071:SF17 | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | 29 | 421 | 2.8E-56 |
| 3 | g567.t1 | PANTHER | PTHR15071 | MANNOSE-6-PHOSPHATE RECEPTOR FAMILY MEMBER | 342 | 629 | 2.8E-56 |
| 5 | g567.t1 | PANTHER | PTHR15071:SF17 | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | 342 | 629 | 2.8E-56 |
| 1 | g567.t1 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 275 | 406 | 2.6E-17 |
| 2 | g567.t1 | Pfam | PF00878 | Cation-independent mannose-6-phosphate receptor repeat | 413 | 566 | 6.5E-10 |
| 18 | g567.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 19 | g567.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 20 | g567.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 14 | - |
| 22 | g567.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 17 | g567.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 751 | - |
| 21 | g567.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 752 | 772 | - |
| 16 | g567.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 773 | 823 | - |
| 26 | g567.t1 | SMART | SM01404 | CIMR_2 | 3 | 120 | 0.0033 |
| 27 | g567.t1 | SMART | SM01404 | CIMR_2 | 122 | 268 | 2.8E-5 |
| 25 | g567.t1 | SMART | SM01404 | CIMR_2 | 270 | 406 | 8.3E-24 |
| 24 | g567.t1 | SMART | SM01404 | CIMR_2 | 411 | 567 | 1.1E-14 |
| 7 | g567.t1 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 25 | 164 | 9.42E-15 |
| 9 | g567.t1 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 150 | 310 | 4.06E-17 |
| 10 | g567.t1 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 315 | 448 | 1.31E-14 |
| 8 | g567.t1 | SUPERFAMILY | SSF50911 | Mannose 6-phosphate receptor domain | 437 | 611 | 6.15E-23 |
| 11 | g567.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 23 | g567.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 750 | 772 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g567/g567.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g567.t1.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 transcript has been annotated with K06564 (insulin-like growth factor 2 receptor)
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.
