General information for g1881.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine-protein kinase transmembrane receptor Ror.
Parent gene
- The parent gene g1881 is located on chr_3: 13633215..13635966 (- 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 | g1881 | g1881.t1 | TTS | g1881.t1 | 13632247 | 13632247 |
| chr_3 | g1881 | g1881.t1 | isoform | g1881.t1 | 13633215 | 13635966 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon1 | 13633215 | 13633300 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS1 | 13633215 | 13633300 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon2 | 13633358 | 13633558 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS2 | 13633358 | 13633558 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon3 | 13633616 | 13634203 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS3 | 13633616 | 13634203 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon4 | 13634264 | 13634456 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS4 | 13634264 | 13634456 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon5 | 13634517 | 13634789 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS5 | 13634517 | 13634789 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon6 | 13634851 | 13635124 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS6 | 13634851 | 13635124 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon7 | 13635220 | 13635771 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS7 | 13635220 | 13635771 |
| chr_3 | g1881 | g1881.t1 | exon | g1881.t1.exon8 | 13635836 | 13635966 |
| chr_3 | g1881 | g1881.t1 | cds | g1881.t1.CDS8 | 13635836 | 13635966 |
| chr_3 | g1881 | g1881.t1 | TSS | g1881.t1 | 13636270 | 13636270 |
Sequences
>g1881.t1 Gene=g1881 Length=2298
ATGAAACTTTGGTGTAATTATGCAATAATCTTAACATTACTAGTTGCTAATGCATTGCAG
CAACAAATTGAAGATGATAATGTTAGTTTAGAAAATCAACATCAGTTCAATGACACCAGC
AGCATACACAACATTGAAAATGTACCAGAAAATCTTGAGTTTGGCATCTGCCAGATTTAT
ACTGGAAAAATTTGTGAAAGATACATGGGCAATCAATCTGTTTTTATTTCACCCGATTTA
ACAATGGAGATGATTGAAAGTAAACTGTTTGAGGCTGCAGGTGTAATAAAAACTAGTCCA
GATGTATCATCATTGTGTTCAAGATTTGTTTGGTATAGTCTTTGTGCAACTGTTCTTCCC
ATATGCAGAACTCCTGAAGAAACAAATCATATCTATTTTCTTAATAAAAATAAATATAAT
AAAAAAGGTGGCACAGTGCCCATTTTAAATACCAACAATAAGGCTAAAAAATCGAATCCA
CCAAAGAACAAGAAGCAATCAAAAAGCAAATCAACAAATGGAATAAAAATTATTCCAACG
GATGCACCAATTTATGAAATACCAACAACGACAATGAGGCAGAGAATTATTGATCATTAT
CGCAACTCAAACTCATACTATGAAGAAACTGACGGTAAAAATAGACGACGACGAGACATC
GACATTCATTTAGTGAGAAATGGCTTTCCACCCACGAAAGAAACTGAAAATTTGAGACGA
ATATGCAAAACTGATTGTGAATTATTGGAGAATGAAATTTGTCAGAAAGAATATGCTATA
GCAAAACGTCATCCCGTGATAAGTAAAATGTTACCTATTGAAGATTGTAGAGGATTAGAA
GATGAAGATGATTGTTTGAACATGGGGATTGATGTTGATATAAGAGTTGATGACACTTGT
TATTGGGATAATGGAGCTGATTATCGAGGAATTAAAGATAAAACTTTAAATAATAAGCCA
TGCATGCGTTGGTCAAAAGTTCCAAAAGGATTGACACATATTGAATTAGCTGGAAATAAT
TATTGTCGAAATGTTGATCATTCACAAAGACAACCATGGTGTTATGTTGATAGACAGACA
ATAGAATTATGTGACATACCAAAATGTGCTGATAAAATGTGGTTCATCATTATTTGTGCT
CTTGCACTTTTTCTGCTTTTCACTTTCTTATTTACTCTTTTGGTTTGTTGCAAGAAAATG
AGAAAGCAAGGAGTTTCAAATATTCAAAATATGTCGATTGCAAATGTTGACAAGAACAAA
AACATTTATGGAAATTCGAGACATAGTTCACCAATAGAAATGACCTCATTAATAAACACT
AATGGCTTATCAAATCCAAATCAATCAACTCATACTCGTGGTGGTTCAATTATGCGAATC
ACTCAATATCGATTGCAAGATGTCAAATTTGTTGAAGAACTTGGTGAAGGAGCATTTGGA
AAAGTTTATAAAGGCGAGCTGTTTCAAAAGAACGGAGAAAAAGTAACAGTCGCAGTTAAA
GCTTTGAAAGAAAATGCATCGCCAAAGACTCAACAAGATTTTCGTCGTGAAATTGAGCTA
ATTTCTGATTTGAAGCACAACAATATTGTTTGCATCCTTGGAGTTATTCTTAGAGAAGAA
CCACTTTGTATGTTATTTGAATACATGAGCCAAGGAGACTTGCATGAGTTTTTAATTTCA
AACAGCCCAAATGAGGGAAAATATCTCACACAGCAACAGTTTCTCTATATCGCATTACAA
ATTGCCGAAGGAATGGAATATCTTTCTAGCCATCACTACATACATCGCGATCTAGCATCA
CGCAATTGCCTCGTTGGTGAAGATTTAGTTGTAAAAATTTCCGATTTTGGTCTGTCAAGG
GACATTTATTCTTCGGATTATTATCGTGTTCAGTCTAAATCACTTTTACCAATTCGTTGG
ATGTCATCTGAAGCTATTCTTTATGGAAAATTCACAACTGAAAGTGATGTATGGAGTTAT
GGTGTTGTTTTATGGGAAATTTATAGCTATGGAATTCAACCTTATTTTGGCTATAGCAAT
CAAGAGGTCATCAATATGGTTAGAGCACGTCAGCTTTTGTCTTGCCCAGAAGCATGTCCT
AGTGCAGTTTATGCTCTTATGATTGAATGTTGGCACGAGCAAAGCGTTCGCCGTCCTAAT
TTTGCTGAAATCGTACATCGCTTGAAAATGTGGTATCAATCACAAAAGAGACGTGATCAA
ATGGACATGAATGTTGGCAGCATGAACAGAAAGACCTCAACTACTGGCTCTACAATAAGT
GTCCGCTCCTTCAAGTAA
>g1881.t1 Gene=g1881 Length=765
MKLWCNYAIILTLLVANALQQQIEDDNVSLENQHQFNDTSSIHNIENVPENLEFGICQIY
TGKICERYMGNQSVFISPDLTMEMIESKLFEAAGVIKTSPDVSSLCSRFVWYSLCATVLP
ICRTPEETNHIYFLNKNKYNKKGGTVPILNTNNKAKKSNPPKNKKQSKSKSTNGIKIIPT
DAPIYEIPTTTMRQRIIDHYRNSNSYYEETDGKNRRRRDIDIHLVRNGFPPTKETENLRR
ICKTDCELLENEICQKEYAIAKRHPVISKMLPIEDCRGLEDEDDCLNMGIDVDIRVDDTC
YWDNGADYRGIKDKTLNNKPCMRWSKVPKGLTHIELAGNNYCRNVDHSQRQPWCYVDRQT
IELCDIPKCADKMWFIIICALALFLLFTFLFTLLVCCKKMRKQGVSNIQNMSIANVDKNK
NIYGNSRHSSPIEMTSLINTNGLSNPNQSTHTRGGSIMRITQYRLQDVKFVEELGEGAFG
KVYKGELFQKNGEKVTVAVKALKENASPKTQQDFRREIELISDLKHNNIVCILGVILREE
PLCMLFEYMSQGDLHEFLISNSPNEGKYLTQQQFLYIALQIAEGMEYLSSHHYIHRDLAS
RNCLVGEDLVVKISDFGLSRDIYSSDYYRVQSKSLLPIRWMSSEAILYGKFTTESDVWSY
GVVLWEIYSYGIQPYFGYSNQEVINMVRARQLLSCPEACPSAVYALMIECWHEQSVRRPN
FAEIVHRLKMWYQSQKRRDQMDMNVGSMNRKTSTTGSTISVRSFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 30 | g1881.t1 | CDD | cd00108 | KR | 297 | 370 | 8.84804E-20 |
| 29 | g1881.t1 | CDD | cd05048 | PTKc_Ror | 465 | 731 | 0.0 |
| 21 | g1881.t1 | Gene3D | G3DSA:1.10.2000.10 | - | 54 | 141 | 2.2E-10 |
| 20 | g1881.t1 | Gene3D | G3DSA:1.10.2000.10 | - | 220 | 290 | 2.3E-7 |
| 18 | g1881.t1 | Gene3D | G3DSA:2.40.20.10 | Plasminogen Kringle 4 | 291 | 373 | 1.9E-16 |
| 17 | g1881.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 459 | 548 | 1.0E-30 |
| 19 | g1881.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 549 | 754 | 1.5E-58 |
| 40 | g1881.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 150 | 173 | - |
| 3 | g1881.t1 | PANTHER | PTHR24416:SF490 | TYROSINE-PROTEIN KINASE TRANSMEMBRANE RECEPTOR ROR | 82 | 741 | 7.5E-145 |
| 4 | g1881.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 82 | 741 | 7.5E-145 |
| 12 | g1881.t1 | PRINTS | PR00018 | Kringle domain signature | 300 | 315 | 3.9E-7 |
| 10 | g1881.t1 | PRINTS | PR00018 | Kringle domain signature | 316 | 328 | 3.9E-7 |
| 13 | g1881.t1 | PRINTS | PR00018 | Kringle domain signature | 335 | 355 | 3.9E-7 |
| 11 | g1881.t1 | PRINTS | PR00018 | Kringle domain signature | 358 | 369 | 3.9E-7 |
| 7 | g1881.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 546 | 559 | 5.4E-32 |
| 6 | g1881.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 587 | 605 | 5.4E-32 |
| 9 | g1881.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 636 | 646 | 5.4E-32 |
| 8 | g1881.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 655 | 677 | 5.4E-32 |
| 5 | g1881.t1 | PRINTS | PR00109 | Tyrosine kinase catalytic domain signature | 699 | 721 | 5.4E-32 |
| 1 | g1881.t1 | Pfam | PF00051 | Kringle domain | 300 | 369 | 4.4E-13 |
| 2 | g1881.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 469 | 728 | 6.5E-96 |
| 24 | g1881.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 25 | g1881.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 26 | g1881.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 28 | g1881.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 23 | g1881.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 372 | - |
| 27 | g1881.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 373 | 396 | - |
| 22 | g1881.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 397 | 765 | - |
| 36 | g1881.t1 | ProSitePatterns | PS00021 | Kringle domain signature. | 341 | 354 | - |
| 39 | g1881.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 474 | 500 | - |
| 37 | g1881.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 593 | 605 | - |
| 38 | g1881.t1 | ProSitePatterns | PS00239 | Receptor tyrosine kinase class II signature. | 621 | 629 | - |
| 41 | g1881.t1 | ProSiteProfiles | PS50038 | Frizzled (fz) domain profile. | 52 | 288 | 10.706 |
| 42 | g1881.t1 | ProSiteProfiles | PS50070 | Kringle domain profile. | 299 | 369 | 14.354 |
| 43 | g1881.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 468 | 732 | 38.944 |
| 34 | g1881.t1 | SMART | SM00130 | KR_2 | 298 | 371 | 1.9E-18 |
| 33 | g1881.t1 | SMART | SM00219 | tyrkin_6 | 468 | 728 | 6.7E-143 |
| 35 | g1881.t1 | SMART | SM00220 | serkin_6 | 468 | 732 | 7.8E-45 |
| 14 | g1881.t1 | SUPERFAMILY | SSF57440 | Kringle-like | 293 | 378 | 8.22E-22 |
| 15 | g1881.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 460 | 738 | 4.05E-81 |
| 16 | g1881.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 31 | g1881.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 32 | g1881.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 373 | 395 | - |
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:0005524 | ATP binding | MF |
| GO:0006468 | protein phosphorylation | BP |
| GO:0004713 | protein tyrosine kinase activity | MF |
| GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | BP |
| GO:0005515 | protein binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K05122 (receptor tyrosine kinase-like orphan 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.
