General information for g11534.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Semaphorin-5A.
Parent gene
- The parent gene g11534 is located on chr_1: 16896234..16897799 (+ 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_1 | g11534 | g11534.t1 | TSS | g11534.t1 | 16892119 | 16892119 |
| chr_1 | g11534 | g11534.t1 | isoform | g11534.t1 | 16892708 | 16897799 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon1 | 16892708 | 16892733 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS1 | 16892708 | 16892733 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon2 | 16893744 | 16893856 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS2 | 16893744 | 16893856 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon3 | 16893918 | 16894017 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS3 | 16893918 | 16894017 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon4 | 16894667 | 16895273 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS4 | 16894667 | 16895273 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon5 | 16895334 | 16895440 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS5 | 16895334 | 16895440 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon6 | 16895502 | 16896053 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS6 | 16895502 | 16896053 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon7 | 16896115 | 16896183 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS7 | 16896115 | 16896183 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon8 | 16896234 | 16896406 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS8 | 16896234 | 16896406 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon9 | 16896464 | 16896556 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS9 | 16896464 | 16896556 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon10 | 16896609 | 16896690 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS10 | 16896609 | 16896690 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon11 | 16896768 | 16897237 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS11 | 16896768 | 16897237 |
| chr_1 | g11534 | g11534.t1 | exon | g11534.t1.exon12 | 16897297 | 16897799 |
| chr_1 | g11534 | g11534.t1 | cds | g11534.t1.CDS12 | 16897297 | 16897799 |
| chr_1 | g11534 | g11534.t1 | TTS | g11534.t1 | 16898527 | 16898527 |
Sequences
>g11534.t1 Gene=g11534 Length=2895
ATGGAGTGGCTTTGCGTCAAACAGATTGAAATGTCATTATGGCGACTAATAATCATTGCA
ACAACCACACTGCTTACACTTGTATCTGGAACTTTTGAGACAATGTCTCAGAATGATTTT
AGATACTTGTCATATCATGATTTATTGACAACAGCTAGTCGATTTTATGATCAAAATGTA
ACAACCTATTCGCGTTTTCATTTTGATGAGAGCAAAAGTCTTATGTTCGTCGGTGCAAGA
GATCGAATTTATAGATTTTCATTGCAACTTGATTTGATGCAAACAGTTAGTTGGGAAGTT
CCAATCGGTGCTATCAAATTTTGTGTAGCTAAAGGACAGACTGAAAATGATTGCCGCAAC
TACATCATGTCACTTCACACCTTTAATAATAAATTATTTGTCTGCGGAAATTTTGCATTT
TCTCCAAGTTGTTCATGGCGCAAGACAGACACATTGGAATTAATAAAAGAAGAAAAGGGT
TTGATAGCATTCAATCCACGATCAAATATTACAACCTTGGTGACTGATGATGGAAAAATG
TTTATTGGATCAACTATAGATTTTTCTGGTTCTGATTCGGTGATTGCAAGAACAGATCTA
TCAATGGATAGCTCAAAGACGTTGAGAACAAAACAATTCAATAACTTGGAACTTTTCAAT
CCTCATTTCGTTGGGAGTTTTGAGAATGGTGAATTTGTGTATTTTGTATTTCGTGAAGAG
TCCATTGAGATGTCCAGTTTTGGAGAGAAAGCAATTTATTCTCGAATCGGACGAGTTTGT
AAGAGTGATTCAGGTGGATTTCACATTTACAAACACAATTGGTCATCATTCTTGAAAGCG
CGATTGAATTGTTCATTAAATGGTTGTGAAACTCAATTTTATTTTAATGAAGTTCAAGAT
ATTACTTTCATGCCAGATGATAATGAACTTTATGCAACATTCTCAACTCCTGATAATAGC
ATTCAAGGATCAGCCATTTGCGTATTCAATATGAGTGCTATTGAGAAAGCTTTTGATGGA
CCTGTAAAATTTCAAATTTCACCAAATTCACCTATATGGGAAGAAAAGATTATCGAAAAT
AGAGACCAATTTGAATGTAAATTCAAATCATCTTCAAATATTCTTGATGCATCGAAATAT
CAACTTATGTCAAGATCAGTCATTCCCAACACTCATGAACCGTTGTATATTGAGAAATTG
GAAAAATTTGTACATATAGCAGTGACAAAAGTTGCTACAAAACTTCATGAAAATGTTAAA
ATAATTTTTGCTGCTAATTCTGATGGATTTATTAAAAAAATTTCAATACTTCCGCGCACT
AAACAATCATGCCTAATCGAAGTTTTAGAGCCTGAATATGTGGGTATTAAAGTGGAAACA
ATGAAATTCATCAAATCAACTGAATCACTTTATGTCGGTACTAAAGAGTCAATTATGAAA
ATTCCATCACAACACTGTTCTCGGCACTTGTCAAAAGTTTCGTGCATCAATTCAATGGAC
CCTTATTGTGGATGGAATGATTTGACATTGACTTGTGGCATGGCGCCAAATCACAACTCT
TTGACAGATTATTGGTATCAAAATGCAACAACATGTCCAATTTTATCAAGTCCTGTTGAT
GGTGCATGGTCAAGTTGGTCACCCTTTTTTAAATGTATAAAATCTGATCCAAATGGCAGT
TATAGTGAAACTGATTTAGGAAATATTGATTCATGTTTGTGTAGAACAAGAACTTGTGAC
AATCCTGCTCCAAAATATGGCGGTAAACTTTGTGAAGGTCACTCAATAATGGTAACAAAT
TGCACAGAACACGGAGGTTGGAGCGACTGGAGTCCATATGGTCCATGTAGTCAAACTTGT
GGTGTTGCAATAAAAGTTCGTCGAAGAACTTGCAGCAATCCATCGCCAAAGCACAATGGC
AGGACTTGCATTGGTAGCAACCAGCAAGAAATTTATTGCACAGATCTTCCTCCTTGTCCT
TCAAATAATATCAATATGCAAATTGATGGTGGATGGTCAGAATTTAGTGAGTGGAGTGCT
TGTAGCGTCGCTTGTGGTGGTGGATTTAGAATACGTGAGAGAAAATGCAATAATCCTATT
CCACAAAATGGTGGTTTAGAATGTATCGGTTGTAATATTGAATATGAAGAATGTAATAAA
CAAATGTGTAATGAAGTTAAAAAGCTCACTTCATGGACACAATGGTTAGTGTCTAATAAT
TCTGAAAGTGGACATTACTTTGAAAAACGATATCGATACATGTGCAAAGCACCAATTAGT
GATCCAGCAAATTTGAAAATATCACTTTATAAAGAAGAAACACGAGCATGTAGTGTAGGA
GACCCTAAATGTCGTCGAATTAATACCACTTGCGAAGCAACAGTTTGCGACCCTCCCAAA
GATTGCAGTGAATATCAGGAAGAGGCTAGAAAATGCAATGAAATCATTCAGTCAGAGAAA
TTAAATGTAACAAAAGCTGGTCTTGAATTTCATTGGATAGGAATCATAATAGTCTCTTTT
GGACTTTTCTGCATTATTTTAACATTTTTCTCAACTAAATATTTTGTGGAAAAGAAAATT
CACCGATTGAGATCAATACAAGGTTCACCTCATTATCTTTCATCATATCCAAATCAATAC
TCTAGCCTACCGACTAAAGATTATAGTGAAAATAATAAACCAAAACGACAGCCATCATTT
AGTGGCACAAGTACAACTGGTCGTTTAAAAGTAACGAATGGAACATTAAATAAGTCCAAC
AACAATCTTCTAAATCAAAACACACCAAAAATTCTTAAATATCAAAATGACACTGAAATG
TCAACATTGAAAAGAAATTCTGCACTTAATAATATGCGCTTAAAGCAAATTGAAGATGAC
AAAGATAAGTACTAA
>g11534.t1 Gene=g11534 Length=964
MEWLCVKQIEMSLWRLIIIATTTLLTLVSGTFETMSQNDFRYLSYHDLLTTASRFYDQNV
TTYSRFHFDESKSLMFVGARDRIYRFSLQLDLMQTVSWEVPIGAIKFCVAKGQTENDCRN
YIMSLHTFNNKLFVCGNFAFSPSCSWRKTDTLELIKEEKGLIAFNPRSNITTLVTDDGKM
FIGSTIDFSGSDSVIARTDLSMDSSKTLRTKQFNNLELFNPHFVGSFENGEFVYFVFREE
SIEMSSFGEKAIYSRIGRVCKSDSGGFHIYKHNWSSFLKARLNCSLNGCETQFYFNEVQD
ITFMPDDNELYATFSTPDNSIQGSAICVFNMSAIEKAFDGPVKFQISPNSPIWEEKIIEN
RDQFECKFKSSSNILDASKYQLMSRSVIPNTHEPLYIEKLEKFVHIAVTKVATKLHENVK
IIFAANSDGFIKKISILPRTKQSCLIEVLEPEYVGIKVETMKFIKSTESLYVGTKESIMK
IPSQHCSRHLSKVSCINSMDPYCGWNDLTLTCGMAPNHNSLTDYWYQNATTCPILSSPVD
GAWSSWSPFFKCIKSDPNGSYSETDLGNIDSCLCRTRTCDNPAPKYGGKLCEGHSIMVTN
CTEHGGWSDWSPYGPCSQTCGVAIKVRRRTCSNPSPKHNGRTCIGSNQQEIYCTDLPPCP
SNNINMQIDGGWSEFSEWSACSVACGGGFRIRERKCNNPIPQNGGLECIGCNIEYEECNK
QMCNEVKKLTSWTQWLVSNNSESGHYFEKRYRYMCKAPISDPANLKISLYKEETRACSVG
DPKCRRINTTCEATVCDPPKDCSEYQEEARKCNEIIQSEKLNVTKAGLEFHWIGIIIVSF
GLFCIILTFFSTKYFVEKKIHRLRSIQGSPHYLSSYPNQYSSLPTKDYSENNKPKRQPSF
SGTSTTGRLKVTNGTLNKSNNNLLNQNTPKILKYQNDTEMSTLKRNSALNNMRLKQIEDD
KDKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 19 | g11534.t1 | Coils | Coil | Coil | 954 | 964 | - |
| 14 | g11534.t1 | Gene3D | G3DSA:2.130.10.10 | - | 38 | 487 | 4.7E-114 |
| 15 | g11534.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 488 | 535 | 4.6E-7 |
| 18 | g11534.t1 | Gene3D | G3DSA:2.20.100.10 | - | 538 | 603 | 1.3E-10 |
| 16 | g11534.t1 | Gene3D | G3DSA:2.20.100.10 | - | 604 | 659 | 7.4E-16 |
| 17 | g11534.t1 | Gene3D | G3DSA:2.20.100.10 | - | 669 | 723 | 5.2E-19 |
| 31 | g11534.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 887 | 920 | - |
| 5 | g11534.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 60 | 638 | 1.1E-197 |
| 8 | g11534.t1 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 60 | 638 | 1.1E-197 |
| 4 | g11534.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 636 | 708 | 1.1E-197 |
| 7 | g11534.t1 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 636 | 708 | 1.1E-197 |
| 6 | g11534.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 708 | 811 | 1.1E-197 |
| 9 | g11534.t1 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 708 | 811 | 1.1E-197 |
| 1 | g11534.t1 | Pfam | PF01403 | Sema domain | 66 | 463 | 1.9E-94 |
| 3 | g11534.t1 | Pfam | PF00090 | Thrombospondin type 1 domain | 608 | 659 | 3.1E-9 |
| 2 | g11534.t1 | Pfam | PF00090 | Thrombospondin type 1 domain | 673 | 723 | 9.7E-12 |
| 20 | g11534.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 11 | - |
| 24 | g11534.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 12 | 32 | - |
| 22 | g11534.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 829 | - |
| 23 | g11534.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 830 | 856 | - |
| 21 | g11534.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 857 | 964 | - |
| 32 | g11534.t1 | ProSiteProfiles | PS51004 | Sema domain profile. | 40 | 483 | 79.097 |
| 34 | g11534.t1 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 604 | 660 | 12.586 |
| 33 | g11534.t1 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 669 | 724 | 13.394 |
| 27 | g11534.t1 | SMART | SM00630 | sema | 63 | 467 | 3.5E-88 |
| 28 | g11534.t1 | SMART | SM00423 | psinew7 | 485 | 533 | 0.005 |
| 29 | g11534.t1 | SMART | SM00209 | TSP1_2 | 607 | 660 | 3.5E-11 |
| 30 | g11534.t1 | SMART | SM00209 | TSP1_2 | 672 | 724 | 1.9E-16 |
| 13 | g11534.t1 | SUPERFAMILY | SSF101912 | Sema domain | 51 | 489 | 4.45E-107 |
| 10 | g11534.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 485 | 535 | 2.67E-8 |
| 11 | g11534.t1 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 604 | 653 | 4.32E-12 |
| 12 | g11534.t1 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 668 | 720 | 9.42E-16 |
| 26 | g11534.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 35 | - |
| 25 | g11534.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 830 | 852 | - |
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:0030215 | semaphorin receptor binding | MF |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K06841 (semaphorin 5)
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.
