General information for g16687.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine kinase receptor Cad96Ca.
Parent gene
- The parent gene g16687 is located on chr_4: 10512275..10515236 (- 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_4 | g16687 | g16687.t1 | isoform | g16687.t1 | 10512275 | 10515236 |
| chr_4 | g16687 | g16687.t1 | exon | g16687.t1.exon1 | 10512275 | 10512586 |
| chr_4 | g16687 | g16687.t1 | cds | g16687.t1.CDS1 | 10512275 | 10512586 |
| chr_4 | g16687 | g16687.t1 | exon | g16687.t1.exon2 | 10513099 | 10513156 |
| chr_4 | g16687 | g16687.t1 | cds | g16687.t1.CDS2 | 10513099 | 10513156 |
| chr_4 | g16687 | g16687.t1 | exon | g16687.t1.exon3 | 10513406 | 10513545 |
| chr_4 | g16687 | g16687.t1 | cds | g16687.t1.CDS3 | 10513406 | 10513545 |
| chr_4 | g16687 | g16687.t1 | exon | g16687.t1.exon4 | 10513604 | 10514713 |
| chr_4 | g16687 | g16687.t1 | cds | g16687.t1.CDS4 | 10513604 | 10514713 |
| chr_4 | g16687 | g16687.t1 | exon | g16687.t1.exon5 | 10514952 | 10515236 |
| chr_4 | g16687 | g16687.t1 | cds | g16687.t1.CDS5 | 10514952 | 10515236 |
| chr_4 | g16687 | g16687.t1 | TSS | g16687.t1 | NA | NA |
| chr_4 | g16687 | g16687.t1 | TTS | g16687.t1 | NA | NA |
Sequences
>g16687.t1 Gene=g16687 Length=1905
ATGAGACAAATTCACACTTTAGTGTTTATTTTGCTGCTTCTTGCAACAAAATTCTCACGA
GGTTCCGGTCCAGGGACAATTTCAGTTGATAGAAACTGGAGTGTTCCGGAATCAACAAAA
ATTGGACAAATTGTAAAAACTGTGAGGGTCACTGGTGTTGGAAATCGAAGTGTTAGCTAT
TCTTTAGAGACTGACGACACGCTGGGCTTTGGAAATTTTGAAAGTCCATTTTGGATTAAT
CCAAGCACTGGATATGTTTATTTGAATAAAAGTCTTGAAGGATGGAAATCACCAAATCCC
TTCATTTTATCAGTAGCAGCAGATGATGGAAATATTCCAGTAAAAAATCAAGTTCTTGTT
CGAATAATTCCATCAAATGGTCAACAAAATTATCCAAATAGTTTTGAGCCACCATCAAGA
ATTCCATCATTGCCTGATTTTACATCACTTCCATTACCACCAATTCCACCACCATATCAG
ACAACAACAAAAGTCATAACAAAACAACCTGAAATTCGACAAAATAAAACTTATATCGAT
GAAACTACAACCACAACAACAACATCAACGACAATCATCACAACAACAGAGGCTGCAAAG
ACAAAAAATGCCGGCATAAGTCAGCAAACTGCTCTTGTTACAATTCTCATTGCAATTATT
ACAATTTTCCTCATTGCTGCACTTATTGCTATGATAATTTTCCGTAAGCAATTAATGCGA
CCATTTAGTCGAAAATTCAAGAAAAGTAAAGTTGATAAAGCCAAAAAGAGCAACCAAAGT
ATTCAAATTATTACATTATCAAATGAAAGCAGTCGAAATTCAATGGTCATGCAGCACTGG
CAGGGACCATTAGCATACAACAATCGGTATACACCATGGGCTCATGATGACATTCATGGT
CAAATTTCAAATTCAAGTTTCACTTATAGTAGTGGAAATGACATAAAAGTACCAGGTTAT
GACCGTTGGGAATTTCCGCGTCATCGACTGAAGGTTTTTAATATTCTCGGTGAAGGAGCT
TTTGGTCAAGTTTGGCGATGTGAAGCTGCTGATATTGATGGTGTTGAAGGAACTTCAATT
GTAGCATTAAAAACACTGAAAGAAAATGCAACAGAAAGCGAAAAAAAAGATCTCATTTCA
GAACTTCAAGTAATGAAAACACTTGAGCCGCACATCAATGTTGTTCGACTTCTTGGTTGT
TGCACTGAAAAAGATCCAATTTTTGTGATAATCGAATATGTTGCATTAGGAAAATTACAA
ACATTCTTAAGAAATTCAAGAGTTGAAAAAAATTATCATAATGCAAGTGGAAAGTCAAAA
ACTTTAACTTCACGTGATCTTGTGTCTTTTATGTATCAAGTTGCAAGAGGCATGGAATTT
CTTACATCAAGAGGAATCATTCATCGTGATTTAGCAGCTAGAAATATTTTAATTACAGAA
GATTACACGTGCAAAATAGCAGACTTTGGATTTGCACGTGATATTGAAACTTCAACTGTA
TATGAAAGAAAAACTGGTGGCCGGCAGCCAATTAGATGGATGGCCATTGAATCACTTTAT
GACAATATTTTCTCAGTCAAGTCTGATGTTTGGGCATTTGGAATTCTCATGTGGGAAATA
GCAACACTCGGTTCGACTCCATATCCTGGAATGGGAGCTGCAGATGTGATGAAAAAAGTT
CGTGATGGTTATAGACTTGAAAAACCAGAACATACAAGTCGAGAAATTTATAATTATATG
TATTACTGCTGGGATGCAGATCCAAAAAATCGACCAGACTTCTCAGAGATTAGAATCAAT
TTAGATAAACTTCTTTCAACCTCAACTGATTATATTGAGCTTGAAAGATTTCCCGAACAT
GATTATTATAATATTCTACACAATATTAGTGGAGAAAAACTGTAG
>g16687.t1 Gene=g16687 Length=634
MRQIHTLVFILLLLATKFSRGSGPGTISVDRNWSVPESTKIGQIVKTVRVTGVGNRSVSY
SLETDDTLGFGNFESPFWINPSTGYVYLNKSLEGWKSPNPFILSVAADDGNIPVKNQVLV
RIIPSNGQQNYPNSFEPPSRIPSLPDFTSLPLPPIPPPYQTTTKVITKQPEIRQNKTYID
ETTTTTTTSTTIITTTEAAKTKNAGISQQTALVTILIAIITIFLIAALIAMIIFRKQLMR
PFSRKFKKSKVDKAKKSNQSIQIITLSNESSRNSMVMQHWQGPLAYNNRYTPWAHDDIHG
QISNSSFTYSSGNDIKVPGYDRWEFPRHRLKVFNILGEGAFGQVWRCEAADIDGVEGTSI
VALKTLKENATESEKKDLISELQVMKTLEPHINVVRLLGCCTEKDPIFVIIEYVALGKLQ
TFLRNSRVEKNYHNASGKSKTLTSRDLVSFMYQVARGMEFLTSRGIIHRDLAARNILITE
DYTCKIADFGFARDIETSTVYERKTGGRQPIRWMAIESLYDNIFSVKSDVWAFGILMWEI
ATLGSTPYPGMGAADVMKKVRDGYRLEKPEHTSREIYNYMYYCWDADPKNRPDFSEIRIN
LDKLLSTSTDYIELERFPEHDYYNILHNISGEKL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 22 | g16687.t1 | CDD | cd11304 | Cadherin_repeat | 34 | 126 | 6.31452E-10 |
| 23 | g16687.t1 | CDD | cd00192 | PTKc | 334 | 598 | 7.10828E-138 |
| 14 | g16687.t1 | Gene3D | G3DSA:2.60.40.60 | Cadherins | 26 | 123 | 3.0E-8 |
| 12 | g16687.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 286 | 413 | 3.3E-37 |
| 13 | g16687.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 417 | 631 | 2.8E-59 |
| 2 | g16687.t1 | PANTHER | PTHR24416:SF537 | TYROSINE KINASE RECEPTOR CAD96CA | 147 | 634 | 2.3E-215 |
| 3 | g16687.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 147 | 634 | 2.3E-215 |
| 7 | g16687.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 411 | 424 | 1.9E-29 |
| 6 | g16687.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 460 | 478 | 1.9E-29 |
| 5 | g16687.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 509 | 519 | 1.9E-29 |
| 8 | g16687.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 528 | 550 | 1.9E-29 |
| 4 | g16687.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 572 | 594 | 1.9E-29 |
| 1 | g16687.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 332 | 599 | 9.0E-95 |
| 17 | g16687.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 18 | g16687.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 19 | g16687.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 16 | - |
| 21 | g16687.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 16 | g16687.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 210 | - |
| 20 | g16687.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 211 | 234 | - |
| 15 | g16687.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 235 | 634 | - |
| 27 | g16687.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 336 | 364 | - |
| 26 | g16687.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 466 | 478 | - |
| 28 | g16687.t1 | ProSiteProfiles | PS50268 | Cadherins domain profile. | 34 | 147 | 10.024 |
| 29 | g16687.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 330 | 623 | 41.573 |
| 25 | g16687.t1 | SMART | SM00219 | tyrkin_6 | 330 | 601 | 3.1E-121 |
| 9 | g16687.t1 | SUPERFAMILY | SSF49313 | Cadherin-like | 32 | 122 | 2.28E-7 |
| 10 | g16687.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 307 | 598 | 1.13E-80 |
| 11 | g16687.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 24 | g16687.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
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:0016020 | membrane | CC |
| GO:0004713 | protein tyrosine kinase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | BP |
| GO:0005509 | calcium ion binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K04362 (fibroblast growth factor receptor 1)
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.
