Gene loci information

Transcript annotation

  • This transcript has been annotated as Roundabout homolog 2.

Parent gene

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 g5256 g5256.t1 isoform g5256.t1 8179610 8226881
chr_2 g5256 g5256.t1 exon g5256.t1.exon1 8179610 8180354
chr_2 g5256 g5256.t1 cds g5256.t1.CDS1 8179610 8180354
chr_2 g5256 g5256.t1 exon g5256.t1.exon2 8181388 8181648
chr_2 g5256 g5256.t1 cds g5256.t1.CDS2 8181388 8181648
chr_2 g5256 g5256.t1 exon g5256.t1.exon3 8181713 8181890
chr_2 g5256 g5256.t1 cds g5256.t1.CDS3 8181713 8181890
chr_2 g5256 g5256.t1 exon g5256.t1.exon4 8182024 8182470
chr_2 g5256 g5256.t1 cds g5256.t1.CDS4 8182024 8182470
chr_2 g5256 g5256.t1 exon g5256.t1.exon5 8184732 8184957
chr_2 g5256 g5256.t1 cds g5256.t1.CDS5 8184732 8184957
chr_2 g5256 g5256.t1 exon g5256.t1.exon6 8185023 8185297
chr_2 g5256 g5256.t1 cds g5256.t1.CDS6 8185023 8185297
chr_2 g5256 g5256.t1 exon g5256.t1.exon7 8185380 8185578
chr_2 g5256 g5256.t1 cds g5256.t1.CDS7 8185380 8185578
chr_2 g5256 g5256.t1 exon g5256.t1.exon8 8185658 8185750
chr_2 g5256 g5256.t1 cds g5256.t1.CDS8 8185658 8185750
chr_2 g5256 g5256.t1 exon g5256.t1.exon9 8191314 8191484
chr_2 g5256 g5256.t1 cds g5256.t1.CDS9 8191314 8191484
chr_2 g5256 g5256.t1 exon g5256.t1.exon10 8192907 8193149
chr_2 g5256 g5256.t1 cds g5256.t1.CDS10 8192907 8193149
chr_2 g5256 g5256.t1 exon g5256.t1.exon11 8193228 8193310
chr_2 g5256 g5256.t1 cds g5256.t1.CDS11 8193228 8193310
chr_2 g5256 g5256.t1 exon g5256.t1.exon12 8198917 8199118
chr_2 g5256 g5256.t1 cds g5256.t1.CDS12 8198917 8199118
chr_2 g5256 g5256.t1 exon g5256.t1.exon13 8201018 8201295
chr_2 g5256 g5256.t1 cds g5256.t1.CDS13 8201018 8201295
chr_2 g5256 g5256.t1 exon g5256.t1.exon14 8204103 8204233
chr_2 g5256 g5256.t1 cds g5256.t1.CDS14 8204103 8204233
chr_2 g5256 g5256.t1 exon g5256.t1.exon15 8205382 8205520
chr_2 g5256 g5256.t1 cds g5256.t1.CDS15 8205382 8205520
chr_2 g5256 g5256.t1 exon g5256.t1.exon16 8220776 8220953
chr_2 g5256 g5256.t1 cds g5256.t1.CDS16 8220776 8220953
chr_2 g5256 g5256.t1 exon g5256.t1.exon17 8221020 8221138
chr_2 g5256 g5256.t1 cds g5256.t1.CDS17 8221020 8221138
chr_2 g5256 g5256.t1 exon g5256.t1.exon18 8226545 8226881
chr_2 g5256 g5256.t1 cds g5256.t1.CDS18 8226545 8226881
chr_2 g5256 g5256.t1 TSS g5256.t1 NA NA
chr_2 g5256 g5256.t1 TTS g5256.t1 NA NA

Sequences

>g5256.t1 Gene=g5256 Length=4305
ATGTTCTTTTTCATTTTTTTCATTACAGCACAATTCAGATCACCTCGAATCACTGAGCAT
CCGAGTGATATTCTAGTCGCTAAAAATGAGCCTGTGACGCTTAACTGCAAAGCAGAAGGT
CGACCTGATCCAGTCATTGAATGGTTCAAAGATGGTGAACCCGTAAAAACTAGTTCAGTT
GACAGCAAGTCACATCGTGTGCAATTGCCAACTGGTTCATTATTTTTCCTTCGTACAGTG
CATAGCAAGAAGGAACAGGATGGTGGCGTATACTGGTGTGTTGCCAAAAATTCTGCTGGA
AAGAGTGCAAGTCGTAATGCAACATTGCAGATAGCGGTGTTGCGCGATGATTTTCGTATT
GAGCCAAAAGATACTCGTGTAGCAGCAGGTGAAACCGCATTGCTTGAATGTGGACCACCT
AAAGGCAATCCCGAGCCAAAAGTTGAATGGAAAAAAGATGGCGTGTGGATTGATTTGGAT
GATGTTAGAAGCCGCAATAATCGACTAAGAATAGTTGATGGTGGCAATTTATTAATAAAT
AACGTGCAAACTATCGATGAAGGCAAATATCAATGTGTAGCTTCAAACATGGTGGCGAGC
AAGGAAAGTGCTCAAGCTAAATTGACTGTTCAAGTTAAACCGACATTTATCAAAGAGCCA
TCAAATGCGAGCGTCTTAGCAGGCCAAACAGTTCAATTATATTGCTCAGTGACTGGCGAT
CCTCAACCACAAATTTATTGGCGCAAGGAAAATGGAAATATTCCACATGGAAGAGCTGAA
ATTTTGGACGGTGATAAAAGTTTAGTTATAAAGGGCGTTATTGCTAGCGATGAAGGAACA
TACATTTGTGAAGCGCACAATAGTGTCGGTCAAATCAGCTCTAAAGCTCAATTAATTGTT
AATTCACTGCCAGTGTTCGATACAAAACCACAAGATGTGAAGACAGGGATAAATGGTGTG
GCGAAATTTGAGTGTGTTGCATCTGGTAATCCTCAACCATCGGTTTATTGGACAAAAGAA
GGCTCACAGGAGCTCATGTTTCCTGATAACACCTATGGACGTCATCATGTTACACTCGAG
GGTGTGCTTGAAATTAAGGGCGTTAGAAAAGAGGACGCTGGATATTATGTATGTTCGGCA
TTCAGTGTTGCCGGATCAGGTTCAACTAGGGCGTTTTTAGAGGTTAATTCAGTTGATGAT
ATTCCACCACCAATTATAAAAATTGGGCCAACAAATCAGACCCTACCGAAGGGGAGTGTT
GCAACATTATTATGCCGCGCTGCTGGCAATCCAACACCTGAAATTAAATGGTCAAAAGAC
GGAGCACCATTGCATATGAAAAAACGCTTTGAAGTTATTCAAAGTGGAACATTAAAAATT
GACGATTTACATTTAGAAGATACTGGCATATACACATGTACAGCCACATCAGAGAGTGGT
GAAACATCATGGAGCGCTTCGCTCATGGTCGAAAAAAGCTCCACAAGCACTTTGCATCGT
GCACCTGATATTAGTATGCTACCGACATCGCCAAGTGAACCGAAACTAGTAAATGTGACA
GCTACGAGCGTAACACTGTCGTGGAATAAAGTGCAATCGAAGCAGAGCGGTACGACAGCT
TTTATCGGATATTTTGTCGAGTATTTTAGTTCCGATTTGCAAACTGGCTGGATAACAGCA
GCACAAAGAGTGCCCAGCAATGTTGTCACGATTACCGACCTCAAGCCCGGCACATCATAC
ATCTTTCTAGTTCGTGCAGAGAATTCATATGGACTCTCGGAGCCATCGCCTGTGTCGAGT
GTCGTCAAAACACTCGGAACAGACAAAAGCATTGTGCCACCAAACGAACTTGCAGCAGCT
CGTAACATACTTAGTGGAAAGGTTCTGGAATTGACAGATGCTTTGGCAGTTAATTCAACA
GCAGTACGGCTCGAATGGCATCTTTTATTGAGCAATACAGAAGATTACATTGAGGGTTTG
CTCATAAGATATCGTGAATTGCATAGTGGAACACAAAAATTCAATTCTGTCATTGTGACA
GAGCCTGATTTGGAAGTCTACGATGTCGGCAGTCTCAGCAAGTTCACAAAGTATGAATTT
TTCATTTCACCATTTTACCGGACAGTTGAGGGCATGCCGAGTAATTCTAAAATTGTACAA
ACATTGGAGGATGTTCCTACAGCTCCTCCATCAAATGTGCAAGTGGGCATGCTGAATTTA
ACATCAGGCGTTGTCCGTTGGAATCCTCCGCCTCAACAAGATCACAATGGCATTTTGCTT
GGTTATAAAATTCAAGTTAAAGCCGGCAATTCGACAAAAATTCTTGCACAAATGACTTTA
AATGCGACAACGTTATCGGTTGGACTGCATAATTTGACAACAGGTGCCACTTATAATGTT
CGTGTTGTTGCATATACTAGAGTTGGCGCTGGGCCATATTCCAAATCGGTGGCTCTAATT
ATGGATCCATCATTTTTGGTGTCTGCACCTCGTGCACATCCAAGTGGTATTTCAACGGGT
GACACATATCAAAATGATAGTATAATTCATCAACCATGGTTTATGGCTGTCATTGCCATT
GTTCTCGTCATGTTTCTTGTCTCGACTGCATTTACATTGCGCTTCCTATACCGACGTAGG
AAAAATTTATCAAAGGGACTTCAACATTTGAGTGCAGTTCCTACAGCCGTAAATGGTGGC
GACGTGATGATGAATATTAATGGCAAAGAGAGTCTATGGATTGACTTTAAGTCATCAATT
GGGCCCATACAAAATCGTGGTTGGCGTACAGGTGATATGGACAAGGACTCTGGTTTGAGT
GGCATGAAATTACTTGAAAATTCACAATTGGGCTCTACACAAGGCACTTATACCGATTGC
GGTACTGACTATGCAGAAGTTGATCCCCGAAACATGAGCAGCTTCTACAATTGTCGAAAA
TCGCCAGACAATCCAACGCCCTATGCCACAACGATGCTAATTAATTCAATGCCAACGGAA
ATGTGTACAAATCCATCACATTCACATTCTGAGCACGAAATCGGAGCAGGCGGATCATCA
GGCACGTCGAGTTTACATTCCGATGGCAAATACTGCATGCATTCAAAGCATTACAATCCA
GCACCAACAAATTGGATTGATTTTCTTCCACCGCCGCCAATGGGTCCACCACCAATTCCT
GAAATGTCTTCAGATTATGGTTCCGATCCGTTCACAGCAAGTCTCATTCCAAACTGCAAA
AAATCATCGTTGAGCTCCCGCAGTGGCTCTGGACTGTCAGCAAGACAGCAAGCACAAAAC
ATGAACATATCACAAGGGTCCGAATATAACTACAATCATGCGACATCATCAAGTAAAAAT
TCTTCAAATGGCATGCCACCTTTTGCAAATCGACCACTTCCATTTCTATGTCACGAATCA
GCAATGAATCAACAGCAAGCGTACAATCATATGATGAATAACGCTAACTCGTGCTGCCCT
CAGCCACAACAACAATCGATGATGAATGAACATATCTATAATGAATATGAACCATATCAG
CAAAGAAAATTTAATTCCAGATTATGCGATAGCTATGATGCCCTGCCAAATTGTTCCAAT
TCAAAGCAGACGACACCAACAACTCTTCACAATCCGACAAGTTTTGGGTCACTCAACGAT
AACTCGATTTACAAGTGCTCATCGGATTGCTACTCAATGGAACGACAGCCACCACGTCAT
AATCATCATACTCATTCGCATTTCAATAATAATAACAGCAACAGTAGCAACAACAATAAA
AGAAAACAAAAGACTAAACATCATCATAGAAATAACAACAATCAAAAGCAGCAACATTCA
CCACAAGATGCAGTTCCTTCTCCCTATGCTCATCAAACAATTGTCACTACGCCTGATCAA
AGTCATGCAAATTATGAATATATCATAGATAATTCATCACATGGTGATGATGATGAAAAT
TCATGCAATTTAGGCAAAGTGACGATCTCAGAAAATGAAGAAACAACTGAGCATGATGAT
GATGATATTGGCAATAGTTACTCATGTGATGACACTTTGACTGATGATGCTATTTTATCA
ACAGGCAATGATGGTGGACAAATGAAAAACAAGTCAAATGGTCATGGATTTAAGCACAAT
CATAATCATCATTGTGAGCAGACAAGTCGTGATAGTGGAAGTGGTGGCGAAACATGCTGT
TCATGTAGTGACACGTCTTGTGTCTATGAAGAACCACCGAGTCATCTACCACCAACATCA
ACTGTTCAAGCAAATCAAGCACTGAGAATTGGCGATGAAAATTAA

>g5256.t1 Gene=g5256 Length=1434
MFFFIFFITAQFRSPRITEHPSDILVAKNEPVTLNCKAEGRPDPVIEWFKDGEPVKTSSV
DSKSHRVQLPTGSLFFLRTVHSKKEQDGGVYWCVAKNSAGKSASRNATLQIAVLRDDFRI
EPKDTRVAAGETALLECGPPKGNPEPKVEWKKDGVWIDLDDVRSRNNRLRIVDGGNLLIN
NVQTIDEGKYQCVASNMVASKESAQAKLTVQVKPTFIKEPSNASVLAGQTVQLYCSVTGD
PQPQIYWRKENGNIPHGRAEILDGDKSLVIKGVIASDEGTYICEAHNSVGQISSKAQLIV
NSLPVFDTKPQDVKTGINGVAKFECVASGNPQPSVYWTKEGSQELMFPDNTYGRHHVTLE
GVLEIKGVRKEDAGYYVCSAFSVAGSGSTRAFLEVNSVDDIPPPIIKIGPTNQTLPKGSV
ATLLCRAAGNPTPEIKWSKDGAPLHMKKRFEVIQSGTLKIDDLHLEDTGIYTCTATSESG
ETSWSASLMVEKSSTSTLHRAPDISMLPTSPSEPKLVNVTATSVTLSWNKVQSKQSGTTA
FIGYFVEYFSSDLQTGWITAAQRVPSNVVTITDLKPGTSYIFLVRAENSYGLSEPSPVSS
VVKTLGTDKSIVPPNELAAARNILSGKVLELTDALAVNSTAVRLEWHLLLSNTEDYIEGL
LIRYRELHSGTQKFNSVIVTEPDLEVYDVGSLSKFTKYEFFISPFYRTVEGMPSNSKIVQ
TLEDVPTAPPSNVQVGMLNLTSGVVRWNPPPQQDHNGILLGYKIQVKAGNSTKILAQMTL
NATTLSVGLHNLTTGATYNVRVVAYTRVGAGPYSKSVALIMDPSFLVSAPRAHPSGISTG
DTYQNDSIIHQPWFMAVIAIVLVMFLVSTAFTLRFLYRRRKNLSKGLQHLSAVPTAVNGG
DVMMNINGKESLWIDFKSSIGPIQNRGWRTGDMDKDSGLSGMKLLENSQLGSTQGTYTDC
GTDYAEVDPRNMSSFYNCRKSPDNPTPYATTMLINSMPTEMCTNPSHSHSEHEIGAGGSS
GTSSLHSDGKYCMHSKHYNPAPTNWIDFLPPPPMGPPPIPEMSSDYGSDPFTASLIPNCK
KSSLSSRSGSGLSARQQAQNMNISQGSEYNYNHATSSSKNSSNGMPPFANRPLPFLCHES
AMNQQQAYNHMMNNANSCCPQPQQQSMMNEHIYNEYEPYQQRKFNSRLCDSYDALPNCSN
SKQTTPTTLHNPTSFGSLNDNSIYKCSSDCYSMERQPPRHNHHTHSHFNNNNSNSSNNNK
RKQKTKHHHRNNNNQKQQHSPQDAVPSPYAHQTIVTTPDQSHANYEYIIDNSSHGDDDEN
SCNLGKVTISENEETTEHDDDDIGNSYSCDDTLTDDAILSTGNDGGQMKNKSNGHGFKHN
HNHHCEQTSRDSGSGGETCCSCSDTSCVYEEPPSHLPPTSTVQANQALRIGDEN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
28 g5256.t1 CDD cd00096 Ig 421 487 6.98082E-16
30 g5256.t1 CDD cd00063 FN3 508 602 1.42796E-18
31 g5256.t1 CDD cd00063 FN3 636 721 1.11868E-4
29 g5256.t1 CDD cd00063 FN3 729 817 2.51255E-14
23 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 10 114 1.0E-29
24 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 115 209 1.6E-24
21 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 210 302 4.3E-26
18 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 303 400 2.6E-18
17 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 401 498 7.3E-25
20 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 499 608 3.9E-24
22 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 615 726 4.2E-18
19 g5256.t1 Gene3D G3DSA:2.60.40.10 Immunoglobulins 727 852 1.5E-22
51 g5256.t1 MobiDBLite mobidb-lite consensus disorder prediction 1236 1287 -
49 g5256.t1 MobiDBLite mobidb-lite consensus disorder prediction 1260 1274 -
50 g5256.t1 MobiDBLite mobidb-lite consensus disorder prediction 1411 1434 -
8 g5256.t1 PANTHER PTHR13817:SF127 LP22668P 12 977 2.1E-247
9 g5256.t1 PANTHER PTHR13817 TITIN 12 977 2.1E-247
1 g5256.t1 Pfam PF13927 Immunoglobulin domain 15 97 4.0E-15
2 g5256.t1 Pfam PF07679 Immunoglobulin I-set domain 118 210 3.6E-14
5 g5256.t1 Pfam PF07679 Immunoglobulin I-set domain 214 300 2.8E-18
4 g5256.t1 Pfam PF07679 Immunoglobulin I-set domain 304 395 1.9E-13
3 g5256.t1 Pfam PF07679 Immunoglobulin I-set domain 406 490 2.1E-17
7 g5256.t1 Pfam PF00041 Fibronectin type III domain 510 596 1.1E-12
6 g5256.t1 Pfam PF00041 Fibronectin type III domain 729 814 2.9E-14
26 g5256.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 852 -
27 g5256.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 853 877 -
25 g5256.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 878 1434 -
56 g5256.t1 ProSiteProfiles PS50835 Ig-like domain profile. 15 110 14.473
58 g5256.t1 ProSiteProfiles PS50835 Ig-like domain profile. 116 209 12.114
59 g5256.t1 ProSiteProfiles PS50835 Ig-like domain profile. 214 299 13.947
57 g5256.t1 ProSiteProfiles PS50835 Ig-like domain profile. 304 396 11.769
55 g5256.t1 ProSiteProfiles PS50835 Ig-like domain profile. 403 489 14.528
52 g5256.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 510 607 23.542
53 g5256.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 627 724 13.476
54 g5256.t1 ProSiteProfiles PS50853 Fibronectin type-III domain profile. 729 824 21.412
35 g5256.t1 SMART SM00409 IG_3c 21 112 4.8E-8
41 g5256.t1 SMART SM00408 igc2_5 27 100 4.7E-11
37 g5256.t1 SMART SM00409 IG_3c 122 211 3.8E-12
45 g5256.t1 SMART SM00408 igc2_5 128 199 7.2E-10
34 g5256.t1 SMART SM00409 IG_3c 220 301 4.8E-15
44 g5256.t1 SMART SM00408 igc2_5 226 290 4.5E-15
46 g5256.t1 SMART SM00406 igv1_8 230 285 0.013
33 g5256.t1 SMART SM00409 IG_3c 310 396 3.6E-9
43 g5256.t1 SMART SM00408 igc2_5 316 385 2.6E-10
48 g5256.t1 SMART SM00406 igv1_8 320 380 0.44
36 g5256.t1 SMART SM00409 IG_3c 410 491 2.0E-11
42 g5256.t1 SMART SM00408 igc2_5 416 480 2.2E-15
47 g5256.t1 SMART SM00406 igv1_8 420 475 0.16
38 g5256.t1 SMART SM00060 FN3_2 508 593 2.2E-14
40 g5256.t1 SMART SM00060 FN3_2 625 711 4.3
39 g5256.t1 SMART SM00060 FN3_2 726 811 5.5E-8
12 g5256.t1 SUPERFAMILY SSF48726 Immunoglobulin 15 112 1.8E-19
13 g5256.t1 SUPERFAMILY SSF48726 Immunoglobulin 118 220 1.19E-20
14 g5256.t1 SUPERFAMILY SSF48726 Immunoglobulin 212 305 1.02E-23
16 g5256.t1 SUPERFAMILY SSF48726 Immunoglobulin 304 403 2.39E-18
15 g5256.t1 SUPERFAMILY SSF48726 Immunoglobulin 403 491 1.32E-23
10 g5256.t1 SUPERFAMILY SSF49265 Fibronectin type III 505 605 2.18E-20
11 g5256.t1 SUPERFAMILY SSF49265 Fibronectin type III 635 821 5.38E-30
32 g5256.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 853 875 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5256/g5256.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5256.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005515 protein binding MF

KEGG

Orthology

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.

Raw TPM values