General information for g11534.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t3 | isoform | g11534.t3 | 16896234 | 16897237 |
| chr_1 | g11534 | g11534.t3 | exon | g11534.t3.exon1 | 16896234 | 16896406 |
| chr_1 | g11534 | g11534.t3 | exon | g11534.t3.exon2 | 16896464 | 16896556 |
| chr_1 | g11534 | g11534.t3 | cds | g11534.t3.CDS1 | 16896505 | 16896556 |
| chr_1 | g11534 | g11534.t3 | exon | g11534.t3.exon3 | 16896609 | 16896690 |
| chr_1 | g11534 | g11534.t3 | cds | g11534.t3.CDS2 | 16896609 | 16896690 |
| chr_1 | g11534 | g11534.t3 | exon | g11534.t3.exon4 | 16896768 | 16897237 |
| chr_1 | g11534 | g11534.t3 | cds | g11534.t3.CDS3 | 16896768 | 16897236 |
| chr_1 | g11534 | g11534.t3 | TSS | g11534.t3 | NA | NA |
| chr_1 | g11534 | g11534.t3 | TTS | g11534.t3 | NA | NA |
Sequences
>g11534.t3 Gene=g11534 Length=818
GTATCAAAATGCAACAACATGTCCAATTTTATCAAGTCCTGTTGATGGTGCATGGTCAAG
TTGGTCACCCTTTTTTAAATGTATAAAATCTGATCCAAATGGCAGTTATAGTGAAACTGA
TTTAGGAAATATTGATTCATGTTTGTGTAGAACAAGAACTTGTGACAATCCTGCTCCAAA
ATATGGCGGTAAACTTTGTGAAGGTCACTCAATAATGGTAACAAATTGCACAGAACACGG
AGGTTGGAGCGACTGGAGTCCATATGGTCCATGTAGTCAAACTTGTGGTGTTGCAATAAA
AGTTCGTCGAAGAACTTGCAGCAATCCATCGCCAAAGCACAATGGCAGGACTTGCATTGG
TAGCAACCAGCAAGAAATTTATTGCACAGATCTTCCTCCTTGTCCTTCAAATAATATCAA
TATGCAAATTGATGGTGGATGGTCAGAATTTAGTGAGTGGAGTGCTTGTAGCGTCGCTTG
TGGTGGTGGATTTAGAATACGTGAGAGAAAATGCAATAATCCTATTCCACAAAATGGTGG
TTTAGAATGTATCGGTTGTAATATTGAATATGAAGAATGTAATAAACAAATGTGTAATGA
AGTTAAAAAGCTCACTTCATGGACACAATGGTTAGTGTCTAATAATTCTGAAAGTGGACA
TTACTTTGAAAAACGATATCGATACATGTGCAAAGCACCAATTAGTGATCCAGCAAATTT
GAAAATATCACTTTATAAAGAAGAAACACGAGCATGTAGTGTAGGAGACCCTAAATGTCG
TCGAATTAATACCACTTGCGAAGCAACAGTTTGCGACC
>g11534.t3 Gene=g11534 Length=201
MVTNCTEHGGWSDWSPYGPCSQTCGVAIKVRRRTCSNPSPKHNGRTCIGSNQQEIYCTDL
PPCPSNNINMQIDGGWSEFSEWSACSVACGGGFRIRERKCNNPIPQNGGLECIGCNIEYE
ECNKQMCNEVKKLTSWTQWLVSNNSESGHYFEKRYRYMCKAPISDPANLKISLYKEETRA
CSVGDPKCRRINTTCEATVCD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g11534.t3 | Gene3D | G3DSA:2.20.100.10 | - | 7 | 63 | 0.0000000 |
| 17 | g11534.t3 | Gene3D | G3DSA:2.20.100.10 | - | 73 | 127 | 0.0000000 |
| 5 | g11534.t3 | PANTHER | PTHR11036 | SEMAPHORIN | 2 | 42 | 0.0000000 |
| 8 | g11534.t3 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 2 | 42 | 0.0000000 |
| 4 | g11534.t3 | PANTHER | PTHR11036 | SEMAPHORIN | 40 | 112 | 0.0000000 |
| 7 | g11534.t3 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 40 | 112 | 0.0000000 |
| 3 | g11534.t3 | PANTHER | PTHR11036 | SEMAPHORIN | 113 | 184 | 0.0000000 |
| 6 | g11534.t3 | PANTHER | PTHR11036:SF79 | SEMAPHORIN 5C, ISOFORM A | 113 | 184 | 0.0000000 |
| 11 | g11534.t3 | PRINTS | PR01705 | Thrombospondin type 1 repeat signature | 9 | 22 | 0.0000028 |
| 10 | g11534.t3 | PRINTS | PR01705 | Thrombospondin type 1 repeat signature | 92 | 103 | 0.0000028 |
| 9 | g11534.t3 | PRINTS | PR01705 | Thrombospondin type 1 repeat signature | 111 | 122 | 0.0000028 |
| 2 | g11534.t3 | Pfam | PF00090 | Thrombospondin type 1 domain | 12 | 63 | 0.0000000 |
| 1 | g11534.t3 | Pfam | PF00090 | Thrombospondin type 1 domain | 77 | 127 | 0.0000000 |
| 19 | g11534.t3 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 8 | 64 | 12.5860000 |
| 18 | g11534.t3 | ProSiteProfiles | PS50092 | Thrombospondin type-1 (TSP1) repeat profile. | 73 | 128 | 13.3940000 |
| 15 | g11534.t3 | SMART | SM00209 | TSP1_2 | 11 | 64 | 0.0000000 |
| 14 | g11534.t3 | SMART | SM00209 | TSP1_2 | 76 | 128 | 0.0000000 |
| 13 | g11534.t3 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 8 | 57 | 0.0000000 |
| 12 | g11534.t3 | SUPERFAMILY | SSF82895 | TSP-1 type 1 repeat | 72 | 124 | 0.0000000 |
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 |
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.
