General information for g4472.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Proto-oncogene tyrosine-protein kinase receptor Ret.
Parent gene
- The parent gene g4472 is located on chr_2: 2736862..2741717 (- 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_2 | g4472 | g4472.t1 | isoform | g4472.t1 | 2736862 | 2741717 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon1 | 2736862 | 2737475 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS1 | 2736862 | 2737475 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon2 | 2737534 | 2737797 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS2 | 2737534 | 2737797 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon3 | 2737854 | 2739424 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS3 | 2737854 | 2739424 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon4 | 2739493 | 2739838 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS4 | 2739493 | 2739838 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon5 | 2739907 | 2740075 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS5 | 2739907 | 2740075 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon6 | 2740682 | 2740923 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS6 | 2740682 | 2740923 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon7 | 2740985 | 2741473 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS7 | 2740985 | 2741473 |
| chr_2 | g4472 | g4472.t1 | exon | g4472.t1.exon8 | 2741693 | 2741717 |
| chr_2 | g4472 | g4472.t1 | cds | g4472.t1.CDS8 | 2741693 | 2741717 |
| chr_2 | g4472 | g4472.t1 | TSS | g4472.t1 | NA | NA |
| chr_2 | g4472 | g4472.t1 | TTS | g4472.t1 | NA | NA |
Sequences
>g4472.t1 Gene=g4472 Length=3720
ATGCTCGATAATTTTAATATCAAATCAAATGAAATTTCACATTTTCATCAATTTGATTTA
ATTCTCACCGTTCCAATAATTGACAACAATCGACATGTGTACGACAAATTTCCTTTAATC
AAATTGGATGTTCTCGACATGTTTCCATCTAATTCAACACGAAAGTTTAGCATTCAAAAA
AATTTGAATTATTTTCGTTTCGATGAAAGCACAGGAGAATTGTGGTTGAAAGATGGCGAT
GTGATGATGGGCAAAAAATATCGCCAAAACGATATTGTGGTTACATTGAATAATGATGCT
GATATCATTGAGACAGACTTGAGAATAAACTTTGTGGCTTATGAAGATATCAAGTATTTC
TGCGAAAAATCAATGTGTTTTTATGATTCAATAGAATTCTTGGTAATCGAAGACTTTGGA
GAAAGTCTCAAATCAAGAGAAATTGGCGAAGTTGCTCCACGCTTCTACAGACGCTTGTGT
AGAAAATACCATGTGGAATATACTCTTTTGAATGGTTCTGACATTCTTTCAATAAATAAA
AACAACAAATTTGTCACAACTGCACTCATTGATCGAGAGAAATTTGAAGATTTGACAGTC
AATGTTGCATGTCACATCAAATTAGGTTCTTCTTTTACATTTCAAACGGAAAAGCTTTTT
AACTTTACTGTACTTGACCTTAACGATAATCAAATTAAAATTCAAGATAATCATAAAGTC
ACAAACTTGACACTAGAGAGCCAATATTTTAAGCAGGATGATGGAATAAAACATTTCGTT
ATTTTCACTGATGCGGATACGTTTGATGCTAACGATGGAATTGAGATTGAGTTGTTAAAC
GATAAATTGAGTGTTTTTAAAAAGGAATGTATCAACCATACAATGAATAAAGCTGAACAA
ACTCCTTCAACAGTCTTTTATTGCACATTGAAATTTTCGAGGAATGGACATTTTCAAACA
TCACCATATTGTGTAACGTTAAGAGCAACAGAAATTCTCAGAAAAAAGACTTACACTGAA
GATGCAACACTCTGTTTTTATCCACATTTTGAAAAGCTTCCAACACCTGCGCCTCTTAGA
GTCAATGACAAAGGAAGAAAAAGTAAAAAGATTACAGATAACATTGTGACTTTAACATCG
TCTGATACTAATGAAAAAGTGCAGAAATTAATCGATATTGAATATCCAAATGAGATTACT
CTATTGAAAAATGCTTCATATTTTGCTCGCACTACTGAGCCGTTGGCAAAAATAAACGAC
CCAAAAATTGTATTTTCTATCTCAGAAGATCCTACACACATATTTAATATAACAAATCGA
GGTGGCATTATTTATATTCAAAACAGCACTTATCTCAAATCAACGATAGCAGCACGTTAT
AAATTAAATATTTCGTGGCATTTTGAGACTATTGGACAAACTCAAAGCACTTCAATTTAT
ATAAAACTTATTGATGCTGAAAATGATTGTAATGAAACAGTTTCTTGTTCGATATATGAA
ACACAATTTGATTGTGAGAATGCATGTGGTTTTGGGTCAAAGGATGGAAGATGCAAATGG
CGTCCATCTAAAGCTGATGGAAATAAAAATCCAAATATTTCAACTATATACAACACATGT
GTTCCTGATTTAGAAACATGTGCATTGCCTGGTAAAGATTGCGATTATCTTGAAAAAGAA
AGTGAAAGTGCAGGAATCTTTGTGTGCTCACAAGATTGCATTAGAGAATTTCTTGGACTG
CCTGATCCTAAAGCAAAAATTATAAAAGTACCAATCGATCTTATGTGTGCATGCACAGGA
GAATATTCATGTCATTGTGGTAAAGGATTTAACCATACTATGCTGACAAAAACAACACAA
CAAAAAACTCCTGAAATTTTAAAATCACAATCAGTAATTGGATCAGAATATCCTGGAGCT
GTTAAAAAGAATGAATGTGGAACAGTTTGCATAATGATTATGATAGGAAGCCCTGCTTTG
TTGGTTTTCTGTATAATAACTCTGATTACAATGCGTAGAAGATATGTAAAGAAAGTTAAA
AAGCGAATGATGCTGAATGGTTCAACAGTTCATTATAGAGGAAGCAATGACACTGAGATC
ATAAATATTAACATTCTCAATGAAGTGGCAAAGGAAAATTATTTGCAAACTTATCAAAAA
TTTGATTTTGATGCAAAATGGGAAGTTGATAGAACAAAATTGATTCTCGATGTGACATTA
GGTGAAGGTGAATTTGGAAAAGTTCTGAAAGCTTATATAACTGAACTTGATGGAAATGAT
TCAGTAAAAACTGTTGCTGTAAAAACAGTTAAATCAAGCAACAATTCTGTTGAACTTTTG
GCATTGCTTTCTGAATTTCAACTCTTGCAAGAAGTTTCTCATCCGAATGTTATAAAATTG
CTTGGTGCATGCATCAAAAGTGAACCTCCATTGATGATTATTGAATATTGCTGTTTTGGA
TCTTTAAGAAGTTACCTAAGACTCAGTAGAAAATTGGAAGAGTCTGGAGATTTAAATATC
GATGGAATCGAACCAGTAACAGCGAAAGATGTTCTTTCATTTTTGTGGCAAATTTGCAAA
GGCATGGCTTATCTTGCTGACATTAAACTTGTTCATAGAGATCTCGCAGCTCGAAATGTG
CTTCTTGCAGAAGGAAAAGTTTGCAAAATTTCTGATTTTGGTTTAACAAGAGATGTCTAT
GAAGACGATGCTTACTTGAAAAAGAGTAAAGATCGAGTACCTGTGAAATGGATGAGTCCA
GAAAGCTTAGCTGATCATGTTTATACAACAAAAACAGATGTTTGGTCGTTTGGAATTGTT
GGTTGGGAAATTGTTACATTGGGTTCAACCCCATATCCAGGCATCCCACCACAAAACCTT
TATCATTTATTACGATCTGGTTATCGTATGCAACGACCAGAAAATTGTTCCCCAGAAATT
TATATTTTACTTCAAGCTTGTTGGATGGATGATCCTCATGCAAGACCATCATTCAAATCA
TTGGCATCAAAGTTTGAAAGTTTATTGGGAAAATGTACCAAATATTTAGATGTTGATATT
AATGGTGATAGTGCAATCTCAAATCCTCTTTATTTATCTAGTGTTGATGATGATTTACAA
AGCAACAAAACTGAAGAAACTGATCTCGATTATAAAAGAATTATAAAAAATATTGATACA
CTTTGGAAGCCACCAAAATTTAAAACTGATATCTCAAAAGTTGACAACAAAAAATATCTT
CTTAAATATGATGATCAAATTCAGCTTTTGCTGTCACGATATGACAAACCAAAACCACTT
AACGAAGCAAACTTTACAAACAATAACAATAAACTTCGTTATCAAAATGATTTTCATACA
TTCCTAAAACCAAATCGCTATGTGAACACAAGCCCAAGCCAACCTGACTTGCTCTCTCTT
ATTGACAATGATCGTGATCGATTAATGTCTGAATCTCGTTACGATACACCTAGTTTGAGG
AGAATGAAAAGCTATATTGAAATGCGAAATATTGCACGTGTCAGAAGATCATCAAATTCC
AATTCAGATAGTTTTGATGATAACAATAATGAGATGCCTTGTGCAAATAAGCGCACAACT
ATAAATGAGAATCTGAATTTTAATGATTTGGATAAGCTTTTGAAGGCTGACAAGGAGATT
ACCTTTAAATTTTCGAGCTTAAATAATCTCAATCAGCGTTTGACAGAAACTCAATGTTAG
>g4472.t1 Gene=g4472 Length=1239
MLDNFNIKSNEISHFHQFDLILTVPIIDNNRHVYDKFPLIKLDVLDMFPSNSTRKFSIQK
NLNYFRFDESTGELWLKDGDVMMGKKYRQNDIVVTLNNDADIIETDLRINFVAYEDIKYF
CEKSMCFYDSIEFLVIEDFGESLKSREIGEVAPRFYRRLCRKYHVEYTLLNGSDILSINK
NNKFVTTALIDREKFEDLTVNVACHIKLGSSFTFQTEKLFNFTVLDLNDNQIKIQDNHKV
TNLTLESQYFKQDDGIKHFVIFTDADTFDANDGIEIELLNDKLSVFKKECINHTMNKAEQ
TPSTVFYCTLKFSRNGHFQTSPYCVTLRATEILRKKTYTEDATLCFYPHFEKLPTPAPLR
VNDKGRKSKKITDNIVTLTSSDTNEKVQKLIDIEYPNEITLLKNASYFARTTEPLAKIND
PKIVFSISEDPTHIFNITNRGGIIYIQNSTYLKSTIAARYKLNISWHFETIGQTQSTSIY
IKLIDAENDCNETVSCSIYETQFDCENACGFGSKDGRCKWRPSKADGNKNPNISTIYNTC
VPDLETCALPGKDCDYLEKESESAGIFVCSQDCIREFLGLPDPKAKIIKVPIDLMCACTG
EYSCHCGKGFNHTMLTKTTQQKTPEILKSQSVIGSEYPGAVKKNECGTVCIMIMIGSPAL
LVFCIITLITMRRRYVKKVKKRMMLNGSTVHYRGSNDTEIININILNEVAKENYLQTYQK
FDFDAKWEVDRTKLILDVTLGEGEFGKVLKAYITELDGNDSVKTVAVKTVKSSNNSVELL
ALLSEFQLLQEVSHPNVIKLLGACIKSEPPLMIIEYCCFGSLRSYLRLSRKLEESGDLNI
DGIEPVTAKDVLSFLWQICKGMAYLADIKLVHRDLAARNVLLAEGKVCKISDFGLTRDVY
EDDAYLKKSKDRVPVKWMSPESLADHVYTTKTDVWSFGIVGWEIVTLGSTPYPGIPPQNL
YHLLRSGYRMQRPENCSPEIYILLQACWMDDPHARPSFKSLASKFESLLGKCTKYLDVDI
NGDSAISNPLYLSSVDDDLQSNKTEETDLDYKRIIKNIDTLWKPPKFKTDISKVDNKKYL
LKYDDQIQLLLSRYDKPKPLNEANFTNNNNKLRYQNDFHTFLKPNRYVNTSPSQPDLLSL
IDNDRDRLMSESRYDTPSLRRMKSYIEMRNIARVRRSSNSNSDSFDDNNNEMPCANKRTT
INENLNFNDLDKLLKADKEITFKFSSLNNLNQRLTETQC
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g4472.t1 | Coils | Coil | Coil | 1227 | 1239 | - |
| 10 | g4472.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 691 | 818 | 2.3E-31 |
| 11 | g4472.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 819 | 1009 | 2.3E-57 |
| 2 | g4472.t1 | PANTHER | PTHR24416:SF485 | PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET | 217 | 1044 | 1.9E-132 |
| 3 | g4472.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 217 | 1044 | 1.9E-132 |
| 8 | g4472.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 814 | 827 | 4.8E-30 |
| 7 | g4472.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 864 | 882 | 4.8E-30 |
| 4 | g4472.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 913 | 923 | 4.8E-30 |
| 5 | g4472.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 932 | 954 | 4.8E-30 |
| 6 | g4472.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 976 | 998 | 4.8E-30 |
| 1 | g4472.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 736 | 1004 | 1.3E-93 |
| 14 | g4472.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 650 | - |
| 15 | g4472.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 651 | 671 | - |
| 13 | g4472.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 672 | 1239 | - |
| 18 | g4472.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 740 | 768 | - |
| 17 | g4472.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 870 | 882 | - |
| 19 | g4472.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 734 | 1009 | 40.838 |
| 16 | g4472.t1 | SMART | SM00219 | tyrkin_6 | 734 | 1005 | 4.6E-130 |
| 9 | g4472.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 714 | 1002 | 6.97E-75 |
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:0004713 | protein tyrosine kinase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K05126 (proto-oncogene tyrosine-protein kinase Ret)
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.
