General information for g6372.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 g6372 is located on chr_2: 16689486..16699850 (+ 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 | g6372 | g6372.t1 | isoform | g6372.t1 | 16689486 | 16699850 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon1 | 16689486 | 16689546 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS1 | 16689486 | 16689546 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon2 | 16693881 | 16694328 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS2 | 16693881 | 16694328 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon3 | 16694850 | 16694980 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS3 | 16694850 | 16694980 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon4 | 16695694 | 16695834 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS4 | 16695694 | 16695834 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon5 | 16696081 | 16696212 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS5 | 16696081 | 16696212 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon6 | 16696291 | 16697222 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS6 | 16696291 | 16697222 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon7 | 16697285 | 16697404 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS7 | 16697285 | 16697404 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon8 | 16697464 | 16697692 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS8 | 16697464 | 16697692 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon9 | 16697936 | 16698605 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS9 | 16697936 | 16698605 |
| chr_2 | g6372 | g6372.t1 | exon | g6372.t1.exon10 | 16699253 | 16699850 |
| chr_2 | g6372 | g6372.t1 | cds | g6372.t1.CDS10 | 16699253 | 16699850 |
| chr_2 | g6372 | g6372.t1 | TTS | g6372.t1 | 16700007 | 16700007 |
| chr_2 | g6372 | g6372.t1 | TSS | g6372.t1 | NA | NA |
Sequences
>g6372.t1 Gene=g6372 Length=3462
ATGAATATGAAATTGGATATTTTTCTGATTATATTCTCGTGTCTATTCTGTAGTGCTATT
GCATTAAAGGCACCGATTATAATTGAACATCCAACTGATAGTATTCAACCTAGAGATCAC
CCATATACACTAAATTGCAAGGCTGAAGGCACACCCGAGCCTAAAATTGAATGGTTTAAA
GATGGTAAAAAATTAACTATTGAGCCATCGCGTCAAATGCTTCTACCAAGTGGTGACCTG
CTGCTACTATCAGTTTCCAATTCAAAACGCGAAAATGACGGTGGAATTTACTGGTGTGAA
GCAAAAAATGAATTTGGCACAGCAAAAAGTCGGAATGCGACTCTAAGAGTAGCAACATTG
CGTGAGGAATTCCGTTTGCATCCACAGCATTCTTTTGTGGCCGATGGTGATACAGTCATG
TTGGAATGCGGTCCGCCTCGTGGAAATCCTGAGCCGATAATTTCATGGCGTAAAAATGGT
CAGATGATGGACTTGAGTGGATCGAAAAGAATTCGTATTGTTGATGGTGGTAATTTAGTC
ATTCAAAATGCTCAACAGTCAGACGATGGACGTTATCAGTGCATTGCCAAAAATATTGTT
GGAGTACGTGAATCTGATGTTGCTATATTAAAAGTTCAAGTTAAGCCATTTCTTATACGT
GGTCCACAAAATCAGACTGTCGTCACTGGTAGCTCCGTTATTTTCCAATGTCGTGTAGGT
GGTGAACCAATGCCTGATGTGCTTTGGCGTAGAACGGCGTCAGGTGGAAATATGCCTTTA
GATCGAGTACACATACTTGAAGATAGAAGCCTTAAAATTGATAATATTACAATGGAAGAT
GTCGGTGAATATAGTTGTGAAGCTGAGAATTCTGTTGGTGCTATTGTTGCATCTGGAATG
CTTCTTGTTCATTCTCCACCAAAGTTCACAGTTCGTCCCAAAACACAACTCGGTGAATTA
GGTAGTGAAGTATTGTTTGAATGTCAAGCAACTGGCTATCCTGAACCAACACTTTTTTGG
ACAATTGAAGGCAATCGTACATTGATTTTACCTGGTATGAAATCAAAAAATATCGAAGCA
TCATTGACAGCTGATGGTGGTAGTATTTTATCAATTGATGAAATTGATCGAAGTGACAAT
GGCAAAGTGATTGTATGCAGTGCAGTCAATAGTGTTGGCAGTGTCAGCACTCGAGTTGTT
CTCACTGTCAATCTTCAAGATGACACACCACCACCACAAATTGTCCAAGGACCTGTAAAT
CAAACATTACCGATAAAAAGTGTCGCATCATTGCCATGTCGTGCTATTGGAACACCAAAA
CCAATTATTAGTTGGTATAAAGATGGAATTCCAGTTGCACAATCTGATAAAATTACAATT
GATGACAATGGATTGTTGACAATCACAGAATTAAATAAAAATGATGACACTGGACTTTAC
ACATGTGTCGCAAGCAGTAAAAGTGGAAAATCAACATGGAGTGGTTTCTTACGAATTGAA
AGTCCAACAAATCCAAATATCAAATTCTATAGAGCACCAGAACCATCAACGCTTCCAGGC
CAGCCAGGTCGTGCACTGATACTTGATAAGACTGACAACAGTGTAAAATTGACATGGATT
CCAAGTAATGCCTTTGGTGCATCAAGCGTTATTGGCTATAGAATTGAAATGTTTGCTCGT
AATTTGACTGAAACTTGGGTTGAAATTGCAAATCGTATTCAAGACACAACCTACACAATT
GAAGGATTAAGGAGCGGCATCACTTACTATTTTGTTGTTCGTGCTGTAAATTCACATGGA
ATGTCTGGTCCAAGTCAGCTATCAGAACCAGTAACTTTAGGAGTGGATGATACAAACTCC
AATCTGGATTTAAGTGAAGCACGAGCAAGTTTACTATCTGGTGATGTCGTTGAATTGACA
AATGCAACAGCAGTTGAATCAACAACTGCAAAATTAACGTGGGATATAATCAATGGACGA
TATGTCGAGGGATTTTACATCTACGCAAGAAATATTGATGATAATGAAGCATCCATTAAA
ATGTTGACTGTTTTGAATGCTGGAAGTGGAGCTTCATCTTGCAAAATTGGTGGTCTCGAT
AAATTTACGACTTATGAATTCTTCATTGTGCCATTTTATAAATCAGTTGAAGGAAAACCA
TCGAATTCAAAAGTGTCGAGAACTCTTGAAGATGTTCCAACAGAAGCACCATCAGGTATG
GAAGCAAAATTACTGAATACATCAACAGTCTATGTTAAATGGAAGGCACCACCAACAAAA
TCACACAATGGCATTCTCACAGCCTACAATGTCATCGTTCGTGGTGTCAATATATACGAA
AACATCTCAAAAGTCTTGACAAATCTCACAATCGACTCTACACGCTCATCAATCATGTTG
GCAAATTTGACGGAAGGCGTGACATACACAGTCAGCGTCGCATCGATGACAAATGCTGGT
CTCGGTCCGTATGGTGCGCCAATCATTATGCGACTCGATCCGACAACAAAGAAATTAGAC
ACATCATTCACATATCGTTTTCCCCTGCATACTGATCATCTCAACGATTTCCTAACACAG
CCCTGGTTTATTATTCTTTTGGGAACAATCTTAGTCATCATGATGCTCTCATTTGGTGTT
ATGGTCTTCATAAAAAGAAAACATATTTTGGCAAAACAATCATCACTTGGACTGCCATCA
ACTCTTGGTACTATGAAAGTCAACAATTATTGGATGGATCCATCAGGCACTATTTGGAAA
TCGAATCAGCATGTAAAAGATGCACATATTCCCGATTATTCACCAATTTGCACTGCTTTA
CCACCATCAACTACTGTTAATATTGATGATGATTCACGTAATCGTTATATGGCAGTATAT
TCTGAGGGTCCAGCTGAATATGCAGAAGTGTCATCACAATCATATCGTAGTGGACAGCCA
TCACCATCACCCTATGCGACAGCAACGCTAATTGGAAACTCGAAAATCATAAGCAGCGAT
CCACAACGTTTTAATATGTTTTACACTACAGACGTTTATCCGCCAATGAATAATAACAAC
AACGATTACAATAGAAGCATTCATTCAGAATCATATAATAATAATAAAATGAACATTGTT
GAGAATCGAATGGCGAATACAATGATGCCAAATATGTTTAATCAGTATACCAGTGATGAT
TCCAATAAGCGTAATCGTCTGAAGCTCATTAAACCGCAAAATTTTCGAATAAATTTGGGT
GCACAAGGCGAGCAATTGTATGTGAAAGTTGGTGACCTAAATGCAGATCAACAGCAACGG
CAGGGTCAAAGTGGTTCATATACGTGGAATCCACAGCTTAAAAATAATTTTAATATTTAT
GAAAATCAAATGCATCGTCATGAGCAGCAGCAACCACAATTTCATCATGAGAATAGTCAG
AATGCTCAAGAGACTGACACAAAAACGCTTAACTGTGATTAA
>g6372.t1 Gene=g6372 Length=1153
MNMKLDIFLIIFSCLFCSAIALKAPIIIEHPTDSIQPRDHPYTLNCKAEGTPEPKIEWFK
DGKKLTIEPSRQMLLPSGDLLLLSVSNSKRENDGGIYWCEAKNEFGTAKSRNATLRVATL
REEFRLHPQHSFVADGDTVMLECGPPRGNPEPIISWRKNGQMMDLSGSKRIRIVDGGNLV
IQNAQQSDDGRYQCIAKNIVGVRESDVAILKVQVKPFLIRGPQNQTVVTGSSVIFQCRVG
GEPMPDVLWRRTASGGNMPLDRVHILEDRSLKIDNITMEDVGEYSCEAENSVGAIVASGM
LLVHSPPKFTVRPKTQLGELGSEVLFECQATGYPEPTLFWTIEGNRTLILPGMKSKNIEA
SLTADGGSILSIDEIDRSDNGKVIVCSAVNSVGSVSTRVVLTVNLQDDTPPPQIVQGPVN
QTLPIKSVASLPCRAIGTPKPIISWYKDGIPVAQSDKITIDDNGLLTITELNKNDDTGLY
TCVASSKSGKSTWSGFLRIESPTNPNIKFYRAPEPSTLPGQPGRALILDKTDNSVKLTWI
PSNAFGASSVIGYRIEMFARNLTETWVEIANRIQDTTYTIEGLRSGITYYFVVRAVNSHG
MSGPSQLSEPVTLGVDDTNSNLDLSEARASLLSGDVVELTNATAVESTTAKLTWDIINGR
YVEGFYIYARNIDDNEASIKMLTVLNAGSGASSCKIGGLDKFTTYEFFIVPFYKSVEGKP
SNSKVSRTLEDVPTEAPSGMEAKLLNTSTVYVKWKAPPTKSHNGILTAYNVIVRGVNIYE
NISKVLTNLTIDSTRSSIMLANLTEGVTYTVSVASMTNAGLGPYGAPIIMRLDPTTKKLD
TSFTYRFPLHTDHLNDFLTQPWFIILLGTILVIMMLSFGVMVFIKRKHILAKQSSLGLPS
TLGTMKVNNYWMDPSGTIWKSNQHVKDAHIPDYSPICTALPPSTTVNIDDDSRNRYMAVY
SEGPAEYAEVSSQSYRSGQPSPSPYATATLIGNSKIISSDPQRFNMFYTTDVYPPMNNNN
NDYNRSIHSESYNNNKMNIVENRMANTMMPNMFNQYTSDDSNKRNRLKLIKPQNFRINLG
AQGEQLYVKVGDLNADQQQRQGQSGSYTWNPQLKNNFNIYENQMHRHEQQQPQFHHENSQ
NAQETDTKTLNCD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 36 | g6372.t1 | CDD | cd00096 | Ig | 429 | 492 | 6.22794E-14 |
| 39 | g6372.t1 | CDD | cd00063 | FN3 | 519 | 612 | 6.73843E-15 |
| 38 | g6372.t1 | CDD | cd00063 | FN3 | 641 | 728 | 1.17091E-6 |
| 37 | g6372.t1 | CDD | cd00063 | FN3 | 735 | 831 | 1.49357E-8 |
| 28 | g6372.t1 | Coils | Coil | Coil | 1110 | 1130 | - |
| 25 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 22 | 121 | 4.1E-24 |
| 20 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 122 | 212 | 1.2E-21 |
| 27 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 213 | 305 | 6.1E-20 |
| 22 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 306 | 404 | 1.3E-15 |
| 23 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 405 | 501 | 1.6E-20 |
| 24 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 511 | 615 | 3.5E-24 |
| 26 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 623 | 733 | 1.4E-18 |
| 21 | g6372.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 734 | 846 | 9.9E-18 |
| 56 | g6372.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1126 | 1153 | - |
| 55 | g6372.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1134 | 1153 | - |
| 9 | g6372.t1 | PANTHER | PTHR12231 | CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN | 18 | 673 | 0.0 |
| 11 | g6372.t1 | PANTHER | PTHR12231:SF246 | ROUNDABOUT 2, ISOFORM B | 18 | 673 | 0.0 |
| 8 | g6372.t1 | PANTHER | PTHR12231 | CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN | 679 | 992 | 0.0 |
| 10 | g6372.t1 | PANTHER | PTHR12231:SF246 | ROUNDABOUT 2, ISOFORM B | 679 | 992 | 0.0 |
| 1 | g6372.t1 | Pfam | PF13927 | Immunoglobulin domain | 25 | 103 | 1.3E-11 |
| 3 | g6372.t1 | Pfam | PF13927 | Immunoglobulin domain | 125 | 198 | 8.6E-14 |
| 4 | g6372.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 220 | 296 | 1.1E-13 |
| 2 | g6372.t1 | Pfam | PF13927 | Immunoglobulin domain | 306 | 390 | 2.0E-10 |
| 5 | g6372.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 412 | 496 | 1.3E-13 |
| 7 | g6372.t1 | Pfam | PF00041 | Fibronectin type III domain | 525 | 605 | 6.1E-12 |
| 6 | g6372.t1 | Pfam | PF00041 | Fibronectin type III domain | 736 | 824 | 1.0E-10 |
| 31 | g6372.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 23 | - |
| 32 | g6372.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 33 | g6372.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 35 | g6372.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 23 | - |
| 30 | g6372.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 24 | 861 | - |
| 34 | g6372.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 862 | 884 | - |
| 29 | g6372.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 885 | 1153 | - |
| 63 | g6372.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 25 | 116 | 12.695 |
| 62 | g6372.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 122 | 208 | 11.388 |
| 61 | g6372.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 216 | 297 | 11.824 |
| 60 | g6372.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 307 | 402 | 11.116 |
| 64 | g6372.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 412 | 492 | 12.985 |
| 59 | g6372.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 521 | 616 | 19.203 |
| 58 | g6372.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 635 | 731 | 12.702 |
| 57 | g6372.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 736 | 835 | 17.428 |
| 45 | g6372.t1 | SMART | SM00409 | IG_3c | 31 | 118 | 9.8E-5 |
| 50 | g6372.t1 | SMART | SM00408 | igc2_5 | 37 | 106 | 1.8E-8 |
| 46 | g6372.t1 | SMART | SM00409 | IG_3c | 128 | 213 | 1.1E-10 |
| 53 | g6372.t1 | SMART | SM00408 | igc2_5 | 134 | 201 | 2.6E-13 |
| 42 | g6372.t1 | SMART | SM00409 | IG_3c | 222 | 304 | 9.8E-10 |
| 52 | g6372.t1 | SMART | SM00408 | igc2_5 | 228 | 293 | 2.1E-13 |
| 44 | g6372.t1 | SMART | SM00409 | IG_3c | 313 | 404 | 4.9E-5 |
| 51 | g6372.t1 | SMART | SM00408 | igc2_5 | 319 | 393 | 0.0025 |
| 43 | g6372.t1 | SMART | SM00409 | IG_3c | 418 | 500 | 2.2E-6 |
| 54 | g6372.t1 | SMART | SM00408 | igc2_5 | 424 | 489 | 7.2E-11 |
| 49 | g6372.t1 | SMART | SM00060 | FN3_2 | 519 | 602 | 2.5E-11 |
| 48 | g6372.t1 | SMART | SM00060 | FN3_2 | 634 | 718 | 5.2 |
| 47 | g6372.t1 | SMART | SM00060 | FN3_2 | 734 | 822 | 6.7E-5 |
| 15 | g6372.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 23 | 117 | 5.34E-18 |
| 14 | g6372.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 124 | 222 | 9.99E-21 |
| 17 | g6372.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 215 | 313 | 6.93E-22 |
| 18 | g6372.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 300 | 403 | 3.81E-15 |
| 16 | g6372.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 411 | 500 | 4.39E-20 |
| 12 | g6372.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 515 | 615 | 2.92E-20 |
| 13 | g6372.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 642 | 831 | 3.37E-25 |
| 19 | g6372.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 21 | - |
| 40 | g6372.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
| 41 | g6372.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 862 | 884 | - |
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.
