General information for g6234.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Roundabout homolog 1.
Parent gene
- The parent gene g6234 is located on chr_2: 15516977..15539751 (- 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 | g6234 | g6234.t1 | isoform | g6234.t1 | 15504185 | 15539751 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon1 | 15504185 | 15505019 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS1 | 15504185 | 15505019 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon2 | 15505448 | 15505652 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS2 | 15505448 | 15505652 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon3 | 15506797 | 15506957 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS3 | 15506797 | 15506957 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon4 | 15507019 | 15507355 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS4 | 15507019 | 15507355 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon5 | 15507425 | 15507647 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS5 | 15507425 | 15507647 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon6 | 15508021 | 15509348 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS6 | 15508021 | 15509348 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon7 | 15509412 | 15509542 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS7 | 15509412 | 15509542 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon8 | 15510188 | 15510341 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS8 | 15510188 | 15510341 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon9 | 15513075 | 15513165 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS9 | 15513075 | 15513165 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon10 | 15516977 | 15517164 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS10 | 15516977 | 15517164 |
| chr_2 | g6234 | g6234.t1 | exon | g6234.t1.exon11 | 15539691 | 15539751 |
| chr_2 | g6234 | g6234.t1 | cds | g6234.t1.CDS11 | 15539691 | 15539751 |
| chr_2 | g6234 | g6234.t1 | TSS | g6234.t1 | 15540324 | 15540324 |
| chr_2 | g6234 | g6234.t1 | TTS | g6234.t1 | NA | NA |
Sequences
>g6234.t1 Gene=g6234 Length=3714
ATGGATAAATTACTAATAGTTTGTTGCACAATTATCATATTGCTCATACATCAAATTAAA
GCCTTTCAAACACCAAGAATTATAGAAAATCCAATTGACACAATTGTGCCACGAAATGAT
CCTGTTACTTTAAATTGTAAAGCAGAAGGCTCACCTAGTCCTACTATTATATGGTTTAAG
GATGGTGTGCAGCTAAAAGCATCACAGCATCGAACTTTTTTGCCTACTGGCAGCTTGTTT
TTTCTTAAGGCTGTAAAAAATGATGGTGGTGTATATTGGTGTGAGGCAAAGAATGAATTA
GGTGTGGCAAGAAGTAGAAACGCTACAATGATAGTAGCAGTCCTTCGAGACGAGTTCCGA
TTAGATCCACAAAATACAAGAGTTGCTCAAGGCGATACGGCCATTCTTGAATGTGGTCCA
CCTCGAGGCAGTCCTGAACCGATAGTCTTATGGAAGAAAAATGGTCAGAAAATTGACACA
GACACATCGAAAAGGATCCGAATTGTTGATGGAGCCAATTTAGCGATACAAGACGTTCGA
CAGGGTGATGAAGGTTCATATCAATGCGTTGCTAAAAATGTTGTTGGCATTCGTGAATCA
CTTGCGGCATATCTTAAAGTAAATGTTAAGCCTTTCCTAATTCGAGGTCCAAGCAATCAG
AGTGTAGTCGAGGGATCTTCAGTGACATTTCAGTGTCGAGTGGGTGGTGATCCAATGCCA
GACGTGCTTTGGCGTCGGTCAGCATCAGGTGGAAATATGCCATTAGAACGAGTTCACATT
CTTGAAGACAGAAGTCTGAGAGTTGACAATGTCATAATTGAAGACATTGGAGAGTACAGT
TGTGAAGCAGACAATGCAGTTGGCACAATTACAGCAACTGGAATCCTTAATGTATATTCA
ACACCAACACTTGTCATTCGACCATCGCCCAAAGTTGTAGAAGCTCCGCTCGATGTATCA
TTTGAATGTAAAGCAACTGGCCAACCACAGCCGCTTCTTTTCTGGTCAATTGAAGGAAAT
CGTTCACTTATTTTTCCACCTAATAGTTTTGATCGTTTTGAAACAACCACAACACCAGAA
AGTTCTTCAATTCTTACTCTACCAACAACAGCTAAAAGTGACAATGGTCTGGTTGTGGTT
TGCAGTGCTGTCAATGCTGTTGGATCGATAAGTGTTCGTGCACGATTGACCATCACATCA
CAAGAAGATAAACCACCACCGATAATTCTTCTTGGTCCAGTCAATCAAACACTGCCTGTA
AAATCAATGGTGAATTTGAATTGCAAAGCTACTGGCAGTCCTACACCAATCATTAGTTGG
TATCGTGATGGAAATCCTGTCGTCAATTCAGAGCGCGTTAATATATCAGATTCAGGAAAT
TTGTTGATTTTTGATCTTGATAAAAATGTTGATCAAGGATTGTACACTTGTGTAGCGAGT
AGTAGAAGTGGGAAATCAACTTGGTCTGGCTATTTAAAGCTTGACTATCCGACAAATCCA
AATATAAAATTCTTTAGAGCGCCAGAATCAGCCGCATTTCCTTCAGCACCAGGCAAGCCT
GAATTTACAAATATTACAGACCACTCAATCACAATTTCATGGCTACCAAGTGTGAAACCT
GGTGCTGGTGAAATTATAGGGTACACAGTGGAAGTTTTTCCTAATGACAACACAAAAGGA
TGGATTACAATTGCACAGAGAATTGAAAGTCTTTCATATACTCATGAGAATGTTGCAAAA
GATTTGACATACATTTATATTGTGAGAGCTGAAAATAGCTTTGGTCTCGGCATGCCATCA
CCTATGTCAGAAGCAATATCTGTCGGAAAAGATTTTAATATCGTTGATGATATAAGTTTA
AGTGAAGCACAGGCCATCTTATCGACCGGCAAAGTGGTCAACTTGTTGGAAGCAAATGCA
ACAGATTCCACAAGTGTAAGACTTGTGTGGGAAATCGTAAATACACAATATGTTGAGGGT
TTCTATATTTACTCCATAAAAGTGAACTCGAATGGAGTTTATAAAATGTTGACAACATTG
CACGGAGGCGGTGCATCAGCTTGCACAATCACACAATTAGAGCGCAACACAATGTACAAC
TTCTTCCTCATACCGTTTTATAAGAGCATTGAGGGAAAGCCATCCAATTTAATACAAACT
GCTACACTCGAGGACGTACCAAGTGTAGCACCATCAAATATGGAAGCAGTCTTACTTAAT
GCAACTGCTGTCTATTTAAAATGGCAACCGCCTGCACCAGAAAACCTTAATGGAAATTTA
AGAAATTATCATGTCATCATTAGAGGCTATGATGCAAATAACATATCAAAAGTTCTCACA
AACATGACAGTCGATGGAAATTCACCCAAATTGATGCTTACAAATCTCACCGCTGGCGTT
ACATATTCAGTAAGTGTAGCAGCTTCAACCAAAGTCGGTTATGGTCCATATAGTTCGCCT
TCAATTCTCCGACTCGATCCGAGTACAAATAAATTGGATCAGGGTTATACGAGATATCCA
ATCAGTCGCGATTATTCTGACGATATCATCACGCAGACCTGGTTTATAATATTGTTAGGC
TCAATTATAGCGATTATTGTTTTCCTGTTTGGCGCTACAGTTTTGTTCAGGAAAATACAG
TACATCAAGCACAATTCGTTAACGAGCGTGCACGGAAATCACGCTATAGGAACGGTGAGA
AAATTTCCGACATTGCCACTGAATGCAAATGGAGTTTGGATTGATCCGACTGGTGGTGTA
TGGCGACAAGCGACAGACGTTCAAAGTATTGGAACAAATGGAATGAAATCTGAAGGAAAT
ATTTCAACAGCAGCAGCTACTGCTCAGGCACCACAACTTCCACTTCCTGACTACGAAAGA
TTAAGTCCATTAAACATGCCTGATTATGCAGAAGTAGCCAACTGTTCATCATTTAAAAAC
TCAAATTCACCGACATACGATTCGTTTGGTGCCTATGCAACCACAACACTCGTTGGTCGT
CAATTTCCAAACAATAATTCTTATTCAGCACCAAACAGTGTTCATTACAATAATTTTATC
AATAGTAACGGTCTAGCGCTTGCACAGAATGGAAATCTTCATCAACAGCAGCAGCATATG
AATGGTGTCAATGGCTCCACAAATAGTCATCTAAAAATGAATATCATCGAGAACAAAATG
GAACAATTGATGAACAATCTAAATAATCCTACAATTGCTACGAATGGCAATGGCATTTCA
CAATCCTCGCATGCCATGAACATGAATCTCAATGCGTCACCCATTGTCTCGATGAAGAAC
GGAACGAAGAGTGTTCCACAGACTCCATTGCTCAGCACAATGCGACGAAATCGTCTTAAT
AATAATGGCAGTATTAATTCCAATAATAAAAGCAATAAATTGTCCTCATCGTCGTATTTG
AGTGAGAAAACAAATTACGGTGTTGATGCGACAGCGGCAGAAATTCAGCCATTGTTCATG
AAATCAAAATTTGATGGTAGTTGGGCATCAATTCCATCGACTAGCGCTTTAACATCATCA
ACAACGACTACAAATAGTAATAACAATAGTCCAAGTCATTTGCCCTTCTCTGTCGCATCT
CCACGTCATCATCATCTCTCCTCACAGCAACTCAATGGCGAAGCTGAAAGACAGGCAATG
ATGAAGGGCAATAATAGCTATTTAAGCAGTTTTGGTCGAAATGACAAAGTGTAG
>g6234.t1 Gene=g6234 Length=1237
MDKLLIVCCTIIILLIHQIKAFQTPRIIENPIDTIVPRNDPVTLNCKAEGSPSPTIIWFK
DGVQLKASQHRTFLPTGSLFFLKAVKNDGGVYWCEAKNELGVARSRNATMIVAVLRDEFR
LDPQNTRVAQGDTAILECGPPRGSPEPIVLWKKNGQKIDTDTSKRIRIVDGANLAIQDVR
QGDEGSYQCVAKNVVGIRESLAAYLKVNVKPFLIRGPSNQSVVEGSSVTFQCRVGGDPMP
DVLWRRSASGGNMPLERVHILEDRSLRVDNVIIEDIGEYSCEADNAVGTITATGILNVYS
TPTLVIRPSPKVVEAPLDVSFECKATGQPQPLLFWSIEGNRSLIFPPNSFDRFETTTTPE
SSSILTLPTTAKSDNGLVVVCSAVNAVGSISVRARLTITSQEDKPPPIILLGPVNQTLPV
KSMVNLNCKATGSPTPIISWYRDGNPVVNSERVNISDSGNLLIFDLDKNVDQGLYTCVAS
SRSGKSTWSGYLKLDYPTNPNIKFFRAPESAAFPSAPGKPEFTNITDHSITISWLPSVKP
GAGEIIGYTVEVFPNDNTKGWITIAQRIESLSYTHENVAKDLTYIYIVRAENSFGLGMPS
PMSEAISVGKDFNIVDDISLSEAQAILSTGKVVNLLEANATDSTSVRLVWEIVNTQYVEG
FYIYSIKVNSNGVYKMLTTLHGGGASACTITQLERNTMYNFFLIPFYKSIEGKPSNLIQT
ATLEDVPSVAPSNMEAVLLNATAVYLKWQPPAPENLNGNLRNYHVIIRGYDANNISKVLT
NMTVDGNSPKLMLTNLTAGVTYSVSVAASTKVGYGPYSSPSILRLDPSTNKLDQGYTRYP
ISRDYSDDIITQTWFIILLGSIIAIIVFLFGATVLFRKIQYIKHNSLTSVHGNHAIGTVR
KFPTLPLNANGVWIDPTGGVWRQATDVQSIGTNGMKSEGNISTAAATAQAPQLPLPDYER
LSPLNMPDYAEVANCSSFKNSNSPTYDSFGAYATTTLVGRQFPNNNSYSAPNSVHYNNFI
NSNGLALAQNGNLHQQQQHMNGVNGSTNSHLKMNIIENKMEQLMNNLNNPTIATNGNGIS
QSSHAMNMNLNASPIVSMKNGTKSVPQTPLLSTMRRNRLNNNGSINSNNKSNKLSSSSYL
SEKTNYGVDATAAEIQPLFMKSKFDGSWASIPSTSALTSSTTTTNSNNNSPSHLPFSVAS
PRHHHLSSQQLNGEAERQAMMKGNNSYLSSFGRNDKV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 33 | g6234.t1 | CDD | cd00096 | Ig | 424 | 487 | 1.26173E-13 |
| 35 | g6234.t1 | CDD | cd00063 | FN3 | 514 | 606 | 4.68773E-13 |
| 34 | g6234.t1 | CDD | cd00063 | FN3 | 636 | 722 | 3.73124E-4 |
| 36 | g6234.t1 | CDD | cd00063 | FN3 | 730 | 824 | 4.90854E-12 |
| 25 | g6234.t1 | Coils | Coil | Coil | 1237 | 1237 | - |
| 22 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 21 | 116 | 9.6E-24 |
| 24 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 117 | 210 | 6.9E-22 |
| 20 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 211 | 301 | 3.6E-19 |
| 21 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 302 | 401 | 6.7E-11 |
| 23 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 402 | 495 | 1.9E-19 |
| 19 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 509 | 611 | 3.6E-21 |
| 18 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 620 | 727 | 1.0E-14 |
| 17 | g6234.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 728 | 838 | 1.7E-21 |
| 51 | g6234.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1106 | 1138 | - |
| 7 | g6234.t1 | PANTHER | PTHR13817:SF127 | LP22668P | 12 | 1093 | 0.0 |
| 8 | g6234.t1 | PANTHER | PTHR13817 | TITIN | 12 | 1093 | 0.0 |
| 1 | g6234.t1 | Pfam | PF13927 | Immunoglobulin domain | 25 | 98 | 3.6E-15 |
| 4 | g6234.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 119 | 200 | 3.5E-13 |
| 2 | g6234.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 215 | 298 | 3.6E-13 |
| 3 | g6234.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 414 | 489 | 4.9E-12 |
| 5 | g6234.t1 | Pfam | PF00041 | Fibronectin type III domain | 515 | 600 | 2.3E-9 |
| 6 | g6234.t1 | Pfam | PF00041 | Fibronectin type III domain | 730 | 818 | 3.0E-12 |
| 28 | g6234.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 21 | - |
| 29 | g6234.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 30 | g6234.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 16 | - |
| 32 | g6234.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 21 | - |
| 27 | g6234.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 22 | 853 | - |
| 31 | g6234.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 854 | 876 | - |
| 26 | g6234.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 877 | 1237 | - |
| 56 | g6234.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 25 | 109 | 13.53 |
| 59 | g6234.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 117 | 208 | 11.043 |
| 58 | g6234.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 211 | 297 | 12.459 |
| 57 | g6234.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 302 | 397 | 9.5 |
| 55 | g6234.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 406 | 487 | 11.987 |
| 52 | g6234.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 516 | 611 | 18.88 |
| 53 | g6234.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 631 | 725 | 11.109 |
| 54 | g6234.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 730 | 828 | 20.734 |
| 42 | g6234.t1 | SMART | SM00409 | IG_3c | 31 | 113 | 1.2E-9 |
| 50 | g6234.t1 | SMART | SM00408 | igc2_5 | 37 | 101 | 7.0E-14 |
| 38 | g6234.t1 | SMART | SM00409 | IG_3c | 123 | 208 | 1.4E-9 |
| 46 | g6234.t1 | SMART | SM00408 | igc2_5 | 129 | 196 | 2.1E-11 |
| 39 | g6234.t1 | SMART | SM00409 | IG_3c | 217 | 299 | 6.6E-10 |
| 48 | g6234.t1 | SMART | SM00408 | igc2_5 | 223 | 288 | 7.3E-13 |
| 41 | g6234.t1 | SMART | SM00409 | IG_3c | 308 | 399 | 7.8 |
| 47 | g6234.t1 | SMART | SM00408 | igc2_5 | 318 | 388 | 2.6 |
| 40 | g6234.t1 | SMART | SM00409 | IG_3c | 413 | 497 | 2.1E-5 |
| 49 | g6234.t1 | SMART | SM00408 | igc2_5 | 419 | 484 | 3.2E-8 |
| 43 | g6234.t1 | SMART | SM00060 | FN3_2 | 514 | 597 | 1.7E-9 |
| 45 | g6234.t1 | SMART | SM00060 | FN3_2 | 629 | 712 | 1.8 |
| 44 | g6234.t1 | SMART | SM00060 | FN3_2 | 728 | 815 | 1.4E-7 |
| 15 | g6234.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 24 | 113 | 2.52E-21 |
| 13 | g6234.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 119 | 214 | 6.89E-20 |
| 11 | g6234.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 210 | 306 | 1.24E-20 |
| 14 | g6234.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 296 | 398 | 9.23E-11 |
| 12 | g6234.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 406 | 495 | 2.53E-19 |
| 10 | g6234.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 512 | 605 | 2.06E-19 |
| 9 | g6234.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 637 | 825 | 2.09E-28 |
| 16 | g6234.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 37 | g6234.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 854 | 876 | - |
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:0005515 | protein 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. There were no conditions that were differentially expressed