General information for g6379.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 g6379 is located on chr_2: 16777383..16790221 (+ 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 | g6379 | g6379.t1 | isoform | g6379.t1 | 16777383 | 16790221 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon1 | 16777383 | 16777432 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS1 | 16777383 | 16777432 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon2 | 16781410 | 16781540 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS2 | 16781410 | 16781540 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon3 | 16781865 | 16782005 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS3 | 16781865 | 16782005 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon4 | 16782702 | 16782833 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS4 | 16782702 | 16782833 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon5 | 16783022 | 16783361 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS5 | 16783022 | 16783361 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon6 | 16783439 | 16783674 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS6 | 16783439 | 16783674 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon7 | 16784855 | 16785135 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS7 | 16784855 | 16785135 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon8 | 16786969 | 16787088 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS8 | 16786969 | 16787088 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon9 | 16787205 | 16787454 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS9 | 16787205 | 16787454 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon10 | 16787740 | 16788249 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS10 | 16787740 | 16788249 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon11 | 16788954 | 16789146 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS11 | 16788954 | 16789146 |
| chr_2 | g6379 | g6379.t1 | exon | g6379.t1.exon12 | 16789459 | 16790221 |
| chr_2 | g6379 | g6379.t1 | cds | g6379.t1.CDS12 | 16789459 | 16790221 |
| chr_2 | g6379 | g6379.t1 | TSS | g6379.t1 | NA | NA |
| chr_2 | g6379 | g6379.t1 | TTS | g6379.t1 | NA | NA |
Sequences
>g6379.t1 Gene=g6379 Length=3147
ATGATAATAATAAATGAAGAAAGAAGAAAAGTAAAGTGCCAAGGCTTAGAAGTACGTATT
GTCGATGGCGGTAATTTGATGATACAAGACGCAAGACAATCCGATGATGGTCGTTATCAA
TGTATTGCTAAAAATATTGTTGGTGTTCGAGAATCAGCAATTGCTTTTCTGAAAGTTCAT
GTAAAACCCTTTCTCATACGTGGTCCACAAAATCAAACAGCCATAACGGGCAGTTCTGTG
GTATTTCAATGTCGTGTGGGTGGTGAACCATTGCCTGATGTTTTATGGCGTAGAACTGCG
TCAGGTGGAAATATGCCCTTAGGTCGAGTTCACATACTCGAAGATAGAAGCTTGAAAATT
GATAACATAACGATGGACGATATTGGTGAATATAGTTGTGAAGCAGACAATGCAGTAGGC
ACTGTTGTTGCATCTGGAATGCTTCTTGTTCATTCTCCACCAAGTTTCACAATTCGACCA
AAATCTCAAGTAGGAGAATTAAATGGCGAAGTAATTTTTGAATGTCAAGCAACTGGCTAT
CCTGAACCAACACTTTTTTGGACAATTGAAGGCAATCGTACATTGATTTTACCTGGTATA
AAATCAAAAAATATCGAAGCATCATTGACAGCTGATGGTGGTAGTATTTTATCAATTGAC
GAAATTGATCGAAGTGACAATGGCAAAGTGATTGTATGTAGTGCAGTCAATAGTGTTGGC
AGTGTCAGCACTCGAGTTGTTCTCACTGTCAATCTTCAAGATGACACACCACCACCACAA
ACATTCAAGGACCTTTGGTATAAAGATGGAATTCCAGTTGCACAATCTGATAAAATAACA
ATTGATGACAATGGATTGTTGACAATTACGGAATTAAATAAAAATGATGACACTGGACTT
TACACATGTGTCGCAAGCAGCAAAAGTGGAAAATCAACATGGAGCGGATTTCTTAAGCTC
GAGAATCCAACAAATCCAAATATTAAGTTCTTCCGAGCACCCGAATCATCAACGTTTCCT
GGCCAACCTGGAAAACCAGAATTAATCGAAAAGACTGACAATAGTGTAACTTTATCATGG
ATCAGAAGTAATGCAATTGGAGCTTCAAGTTTGCTTGGTTACAGTGTCGAAATGTTTGGA
AGAAATTCAACGGATGGTTGGGTGCAAATCGCAAATCGAATACAAAATACAACTTACAAA
GTTCTTGGATTAACGAGTGGTGTTTCTTACTACTTTGCCGTACGTGCAGAAAATTCTCAT
GGCATGTCAGGACCAAGTCAACTGTCGGAACCAATTACTGTTGGAATGATGGATGAAACA
AATACTGACTTGGATCTGAGCGAGGCACGAGCAAGTCTGCTATCCGGCGATGTTGTGGAG
CTAATTAATGCAACATCTGTTGATTCAACAAGTATGAAATTATTATGGGAGATTATAAAT
GGAAAATATGTTGAAGGATTTTACATTTATGCTCGCAACATTGATGATGCTATAGAGGGC
GATAATCATCAGGGTTCATATAAAATGCTGACAATATTAAATGCGGGAAGTGGAGGAGCT
TCATCATGCAAAATTAGCGGATTACAAAAATTTACCACGTACGAGTTTTTTATCGTGCCA
TTTTATAGAACCGTTGAGGGCAAACCATCAAATTCGAGAATTGCTCGAACACTTGAAGAT
GTTCCAAGTGAGCCACCATCAAATATGGAAGCTAAATTACTCAATGTTTCAACAGTTTAT
GTTAAATGGAAAGCACCACCAACAAAATCACACAACGGTATTCTCAAATTCTACAACGTA
ATTGTACGTGGCGTGAATATTTATGAGAATATCTCAAAAGTACTGACAAACATCACAATT
GACGCATCGAGTTCATCAATCATGTTAGCAAATCTCACAGAAGGTGTAACATACACAGTG
AGTGTCGCTGCCATCAACAGGATTGGATTAGGTCCATACAACCAGCCATCCATTTTACGA
CTCGATCCAATTACAAAACGATTAGACACAACATTCACAAATCGTTTTCCGCTCAACAAT
GAGCACATGTCAGATGACTTCCTCACTCAGCCATGGTTCATTATTCTCTTGGGCACAATT
CTAGTCATTATGATGCTCTCATTCGCTATCATGGTGTTTATTAAACGAAGGCACATGTTG
ATGAAACAGTCTGCATTCAATGGTCTCGCAGGACCATCTGCAGGAGGAGCTGTAAAAATA
GCAAATAAGCCAGGAGGCAATGATGGATATTGGCTGGATCCATCTGGAATTGTTTGGCGT
TCAAATTCAAGATCTAAGGGTAGTTTAATACCGGATTATGCGCCCGTTTGCACATCGACC
ACGACAACGACACTTCCGGCTGATGATGAAGCTGTTCGATCTCGATTTATGGGAGAATAT
ACAGACTATCCAGCCGATTATGCAGAAGTATCATCATTTCAAAGTGGTCAACAGTCGCCT
GCTCCATATGCTACAACAACATTAATTGGCAGCTCGAAATTCGCACCAAATGAAGCGCAT
CGTTTCAACATGTTCTATAAAACGGACATTTATCCTCCGCCAAGCAATGTTGGCAATGGT
TCAATGAGACAGCAACAAACGAATAGCAATAATAGTAATAATTACAATAGAAGCATCCAT
TCAGAATCATATTGCAATAATAACAAAATAAATATTGTTGAGAATCGAATGTGTGCTGGC
ACAATGATGCCAAATATGTTTAATCAGCAACACAGCCATAATGGAATTAAAATTGGCTCA
AATAAACGCAATCGTCTGAAACTGATGAAGCCACAAAACATACGAAACTATTTTAGCAAC
CCAAATGAACAGTTGTATGTGAAAGTGGGTGAAATAAATCAAGTTGGTCCACATTCGCTT
TCAAATTCATCACAGCAGTCGCATACACCACAATCGCAGAATGGCTCCATCAACTGGAGT
CAACATAACTTTAATTTATACGAGAATCAATTGCATAATCATTTGAATAATGGCGCTACA
GTAAATAATGAACCTGACGACATCCAAAATGATGATAATCATCATCAGCCGAAACAGCAT
GCAAATGATAAAAATGATTTTATTTATACAGGAAATCGTAGCATAATGAGCTATACAAGC
TCCAAGGACTTTCCTGAAAATGTATGA
>g6379.t1 Gene=g6379 Length=1048
MIIINEERRKVKCQGLEVRIVDGGNLMIQDARQSDDGRYQCIAKNIVGVRESAIAFLKVH
VKPFLIRGPQNQTAITGSSVVFQCRVGGEPLPDVLWRRTASGGNMPLGRVHILEDRSLKI
DNITMDDIGEYSCEADNAVGTVVASGMLLVHSPPSFTIRPKSQVGELNGEVIFECQATGY
PEPTLFWTIEGNRTLILPGIKSKNIEASLTADGGSILSIDEIDRSDNGKVIVCSAVNSVG
SVSTRVVLTVNLQDDTPPPQTFKDLWYKDGIPVAQSDKITIDDNGLLTITELNKNDDTGL
YTCVASSKSGKSTWSGFLKLENPTNPNIKFFRAPESSTFPGQPGKPELIEKTDNSVTLSW
IRSNAIGASSLLGYSVEMFGRNSTDGWVQIANRIQNTTYKVLGLTSGVSYYFAVRAENSH
GMSGPSQLSEPITVGMMDETNTDLDLSEARASLLSGDVVELINATSVDSTSMKLLWEIIN
GKYVEGFYIYARNIDDAIEGDNHQGSYKMLTILNAGSGGASSCKISGLQKFTTYEFFIVP
FYRTVEGKPSNSRIARTLEDVPSEPPSNMEAKLLNVSTVYVKWKAPPTKSHNGILKFYNV
IVRGVNIYENISKVLTNITIDASSSSIMLANLTEGVTYTVSVAAINRIGLGPYNQPSILR
LDPITKRLDTTFTNRFPLNNEHMSDDFLTQPWFIILLGTILVIMMLSFAIMVFIKRRHML
MKQSAFNGLAGPSAGGAVKIANKPGGNDGYWLDPSGIVWRSNSRSKGSLIPDYAPVCTST
TTTTLPADDEAVRSRFMGEYTDYPADYAEVSSFQSGQQSPAPYATTTLIGSSKFAPNEAH
RFNMFYKTDIYPPPSNVGNGSMRQQQTNSNNSNNYNRSIHSESYCNNNKINIVENRMCAG
TMMPNMFNQQHSHNGIKIGSNKRNRLKLMKPQNIRNYFSNPNEQLYVKVGEINQVGPHSL
SNSSQQSHTPQSQNGSINWSQHNFNLYENQLHNHLNNGATVNNEPDDIQNDDNHHQPKQH
ANDKNDFIYTGNRSIMSYTSSKDFPENV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 28 | g6379.t1 | CDD | cd00096 | Ig | 246 | 313 | 6.09784E-7 |
| 31 | g6379.t1 | CDD | cd00063 | FN3 | 340 | 433 | 5.81264E-15 |
| 29 | g6379.t1 | CDD | cd00063 | FN3 | 457 | 557 | 5.30746E-6 |
| 30 | g6379.t1 | CDD | cd00063 | FN3 | 564 | 660 | 1.04002E-9 |
| 21 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 3 | 62 | 3.4E-8 |
| 24 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 63 | 152 | 2.6E-18 |
| 23 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 153 | 247 | 2.7E-15 |
| 20 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 248 | 319 | 7.7E-10 |
| 19 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 335 | 436 | 3.7E-23 |
| 18 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 444 | 562 | 1.3E-17 |
| 22 | g6379.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 563 | 673 | 2.5E-19 |
| 7 | g6379.t1 | PANTHER | PTHR12231 | CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN | 18 | 259 | 0.0 |
| 10 | g6379.t1 | PANTHER | PTHR12231:SF246 | ROUNDABOUT 2, ISOFORM B | 18 | 259 | 0.0 |
| 8 | g6379.t1 | PANTHER | PTHR12231 | CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN | 266 | 498 | 0.0 |
| 11 | g6379.t1 | PANTHER | PTHR12231:SF246 | ROUNDABOUT 2, ISOFORM B | 266 | 498 | 0.0 |
| 6 | g6379.t1 | PANTHER | PTHR12231 | CTX-RELATED TYPE I TRANSMEMBRANE PROTEIN | 506 | 831 | 0.0 |
| 9 | g6379.t1 | PANTHER | PTHR12231:SF246 | ROUNDABOUT 2, ISOFORM B | 506 | 831 | 0.0 |
| 3 | g6379.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 67 | 145 | 1.3E-12 |
| 1 | g6379.t1 | Pfam | PF13927 | Immunoglobulin domain | 153 | 237 | 8.0E-10 |
| 2 | g6379.t1 | Pfam | PF07679 | Immunoglobulin I-set domain | 266 | 316 | 2.8E-5 |
| 5 | g6379.t1 | Pfam | PF00041 | Fibronectin type III domain | 342 | 426 | 1.0E-10 |
| 4 | g6379.t1 | Pfam | PF00041 | Fibronectin type III domain | 565 | 653 | 8.7E-11 |
| 26 | g6379.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 691 | - |
| 27 | g6379.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 692 | 714 | - |
| 25 | g6379.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 715 | 1048 | - |
| 46 | g6379.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 63 | 144 | 11.243 |
| 45 | g6379.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 154 | 249 | 10.172 |
| 47 | g6379.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 266 | 313 | 7.994 |
| 44 | g6379.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 342 | 437 | 18.328 |
| 43 | g6379.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 458 | 560 | 11.401 |
| 42 | g6379.t1 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 565 | 664 | 18.083 |
| 33 | g6379.t1 | SMART | SM00409 | IG_3c | 15 | 60 | 96.0 |
| 35 | g6379.t1 | SMART | SM00409 | IG_3c | 69 | 151 | 9.1E-9 |
| 41 | g6379.t1 | SMART | SM00408 | igc2_5 | 75 | 140 | 5.5E-12 |
| 34 | g6379.t1 | SMART | SM00409 | IG_3c | 160 | 321 | 5.8E-5 |
| 40 | g6379.t1 | SMART | SM00408 | igc2_5 | 166 | 240 | 0.011 |
| 39 | g6379.t1 | SMART | SM00408 | igc2_5 | 241 | 310 | 0.29 |
| 36 | g6379.t1 | SMART | SM00060 | FN3_2 | 340 | 423 | 1.6E-10 |
| 37 | g6379.t1 | SMART | SM00060 | FN3_2 | 456 | 549 | 2.3 |
| 38 | g6379.t1 | SMART | SM00060 | FN3_2 | 563 | 651 | 3.6E-7 |
| 15 | g6379.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 19 | 69 | 2.78E-8 |
| 14 | g6379.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 62 | 160 | 3.01E-21 |
| 16 | g6379.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 153 | 252 | 1.17E-14 |
| 17 | g6379.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 264 | 320 | 1.72E-10 |
| 13 | g6379.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 337 | 435 | 7.99E-19 |
| 12 | g6379.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 463 | 660 | 2.16E-27 |
| 32 | g6379.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 692 | 714 | - |
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