General information for g740.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Semaphorin-1A.
Parent gene
- The parent gene g740 is located on chr_3: 5648031..5651387 (- 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_3 | g740 | g740.t1 | TTS | g740.t1 | 5647295 | 5647295 |
| chr_3 | g740 | g740.t1 | isoform | g740.t1 | 5648031 | 5651387 |
| chr_3 | g740 | g740.t1 | exon | g740.t1.exon1 | 5648031 | 5648497 |
| chr_3 | g740 | g740.t1 | cds | g740.t1.CDS1 | 5648031 | 5648497 |
| chr_3 | g740 | g740.t1 | exon | g740.t1.exon2 | 5648931 | 5650328 |
| chr_3 | g740 | g740.t1 | cds | g740.t1.CDS2 | 5648931 | 5650328 |
| chr_3 | g740 | g740.t1 | exon | g740.t1.exon3 | 5650490 | 5650776 |
| chr_3 | g740 | g740.t1 | cds | g740.t1.CDS3 | 5650490 | 5650776 |
| chr_3 | g740 | g740.t1 | exon | g740.t1.exon4 | 5651118 | 5651202 |
| chr_3 | g740 | g740.t1 | cds | g740.t1.CDS4 | 5651118 | 5651202 |
| chr_3 | g740 | g740.t1 | exon | g740.t1.exon5 | 5651276 | 5651387 |
| chr_3 | g740 | g740.t1 | cds | g740.t1.CDS5 | 5651276 | 5651387 |
| chr_3 | g740 | g740.t1 | TSS | g740.t1 | NA | NA |
Sequences
>g740.t1 Gene=g740 Length=2349
ATGGATTTTGCAGTTCAATTCTGCCTTAAATTTTTAACATTGCTGGTATGCTGCACAACC
ATATGTTATACTTGGACATTTTCAGTCACTCCAAATCGGGTCATAAATTACGAGTCGAGT
GGTCACACGTTCCATCTCAATGGCAGTTTTTTTAAATTATTGAATATGGACGATAATTCT
GTCCTCATCGGTGCGAGAAACAACGTGTACAATTTGAGCTTAACGAGATTAACAGAAAAT
GTACAAAATCGTATTGAATGGCAATCGTCGGATGCGCATAAAGAAATGTGTATTTTGAAA
GGAAAAAACACGACCGATTGTCAGAATTACATACGAATTTTTGCACGTGTTTCCGAACGT
CAAATTGTACTTTGTGGTACGAATAGTTTTAAACCAGCATGCCGCTACTACAAAGTCAAT
CCAATTAGCAGCAGTGGCGAAGCACTACCCGTGCATGAAATGATTCAGGAGTTTGAAGGT
GAAGCAATCAGTCCATACTCACCCAATCAGAATAATACCTACATCTATACGAGCGATATA
AATGAACTTTATACAGCTACATCAGTTGGATTTGCTGGCTCACAGCAATTGATTTATCGA
CAGCCACTGCTCACTACAATTCCTAATAGTTATGGAGGCAGTACACCGCAGACCCTCCGC
ACTGAATCTCGTTTTGACATCTTGAATCAGGCCTCGTTTGTAAATGCCATTGAGTACAAC
AATTACATTCTTTTCTTCTTCCGTGAACAAGCCATCGAATATCAGAATTGTGGCAAAACC
ATGTATTCGAGAGTAGCTCGCGTCTGTAAGAACGACAAGGGAGGTCAACACTCATATGCC
GATCGCTTTTCATCTTTCCTTAAAACTCGCTTGAATTGCTCAATGCCCGGTGAATATCCA
TTCTATTTTGATGAGATTCAAGCGACGAGCAAGTTAGTTGATGGTATTTATGGTAATGAT
CGTGATGCGTTGGTGTATACAGTAATGACGACAAATGATAATGCAATTGATGGTTCGGCT
ATTTGTGTCTTCTCAATGAACTCAATATTGGCTGGCTTCGAGGGTCGATTTAAAAATCAA
CGCGATCAGCATTCAACATGGCGAGCAGTTGATGAATCTGAGTTGCCTCCAACACGACCT
GGAAAGTGTGTCGATGACTCGCGAACTCTACCAATGTCCACGATCAATTTCATACTCAAA
AATCCACTTATGAATGATGCAGTTAATCCAATACATGACTCGCCATTACTTGTGCACACT
GGCTCAAATTACAAATTTACATCGATCGCAGTCGATCCACAAGTCGAGACGGCCAGTGGA
AAAATTTATGATGTTATTTTTGTTGGAACCGATAATGGGCAGGTCTTGAAAGTGATAAAT
GCTGGCGATTCATTGAATGAAAATAAGCCAATTGTAATCAGTGAACAGCAGGTATTGCCC
TTTGGCACACGGATCAAGGAACTGAAAGTGTCGAAAGCTACTCAAACGCTTATTGTGATT
GCTGATGATTATGTAAAGTCCATTCCACTACACAACTGTTCAGCACTCAGTCAATGTTCA
CAATGTATTGGTAGTCGTGATTTATATTGCGTTTGGGATAACATCAATCGAGAATGCATA
TTTTATAATAAAACTTCAATAAATAAGAACACGCAGATGTACGTTGAAAGTATCGATGGT
CGTAATGATGTTGTTTGTGGTGACGATATTGTGGTGCCAAGTAAAAATAACAACGCTGTT
AAGAGCAATGCAAATAATAATGTTGTGAATACTCAAACACATGGAATTATTGCCAATAAT
GGTCAGTTGCCAAGTGAAAGTGAAAGCAAGGAAGAACAAGAACATCGACGACACAAGTAT
CATGGTGTCACTGTCATTCAAGCACCTGCACAACAAGGCACAGAGTTCTATGAACCACAA
ATTCAAACTTCAAGTACATCAATCGTACTACTATTAATGATCGCTGGTCTTATAATTGGT
GTCATAATAGGATTTGCTATATCAAAATGTACAGCACGCGATTCAGCGAGAAGTTCCTTT
CCATTTGGAGCTAATGCCGATAATCACAGAAATCATTTAGGATGGCAAGTGCCGAACAAA
CAATTACATTCTCTTCCAACAATGAACAATGGTGGTAAAGATATTAATCTACTGATGAAT
GCAAATGCTTCATCAATAAATAAGGATAGTAAAAAGGACAATTTAGAGTTAGAGTTCTCG
TTAGGAAATAAGGACAAATTACATGAGTGCAAAAATTCAAATGAAAGTCTCGACAAAGAA
ACTTGTAAATCAGCCGTCATTTCAGCGTCCGGTGGTACGCTACAGAAAGTGAAGAAAACA
TACATTTGA
>g740.t1 Gene=g740 Length=782
MDFAVQFCLKFLTLLVCCTTICYTWTFSVTPNRVINYESSGHTFHLNGSFFKLLNMDDNS
VLIGARNNVYNLSLTRLTENVQNRIEWQSSDAHKEMCILKGKNTTDCQNYIRIFARVSER
QIVLCGTNSFKPACRYYKVNPISSSGEALPVHEMIQEFEGEAISPYSPNQNNTYIYTSDI
NELYTATSVGFAGSQQLIYRQPLLTTIPNSYGGSTPQTLRTESRFDILNQASFVNAIEYN
NYILFFFREQAIEYQNCGKTMYSRVARVCKNDKGGQHSYADRFSSFLKTRLNCSMPGEYP
FYFDEIQATSKLVDGIYGNDRDALVYTVMTTNDNAIDGSAICVFSMNSILAGFEGRFKNQ
RDQHSTWRAVDESELPPTRPGKCVDDSRTLPMSTINFILKNPLMNDAVNPIHDSPLLVHT
GSNYKFTSIAVDPQVETASGKIYDVIFVGTDNGQVLKVINAGDSLNENKPIVISEQQVLP
FGTRIKELKVSKATQTLIVIADDYVKSIPLHNCSALSQCSQCIGSRDLYCVWDNINRECI
FYNKTSINKNTQMYVESIDGRNDVVCGDDIVVPSKNNNAVKSNANNNVVNTQTHGIIANN
GQLPSESESKEEQEHRRHKYHGVTVIQAPAQQGTEFYEPQIQTSSTSIVLLLMIAGLIIG
VIIGFAISKCTARDSARSSFPFGANADNHRNHLGWQVPNKQLHSLPTMNNGGKDINLLMN
ANASSINKDSKKDNLELEFSLGNKDKLHECKNSNESLDKETCKSAVISASGGTLQKVKKT
YI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g740.t1 | Gene3D | G3DSA:2.130.10.10 | - | 27 | 511 | 1.8E-144 |
| 8 | g740.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 513 | 570 | 4.5E-8 |
| 3 | g740.t1 | PANTHER | PTHR11036:SF131 | MIP07328P | 12 | 726 | 1.1E-192 |
| 4 | g740.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 12 | 726 | 1.1E-192 |
| 1 | g740.t1 | Pfam | PF01403 | Sema domain | 54 | 491 | 1.8E-119 |
| 2 | g740.t1 | Pfam | PF01437 | Plexin repeat | 512 | 545 | 6.9E-7 |
| 11 | g740.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 12 | g740.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 2 | - |
| 13 | g740.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 3 | 14 | - |
| 15 | g740.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 18 | - |
| 10 | g740.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 647 | - |
| 14 | g740.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 648 | 667 | - |
| 9 | g740.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 668 | 782 | - |
| 20 | g740.t1 | ProSiteProfiles | PS51004 | Sema domain profile. | 26 | 510 | 102.991 |
| 18 | g740.t1 | SMART | SM00630 | sema | 51 | 494 | 1.4E-130 |
| 19 | g740.t1 | SMART | SM00423 | psinew7 | 512 | 567 | 7.0E-6 |
| 6 | g740.t1 | SUPERFAMILY | SSF101912 | Sema domain | 37 | 514 | 8.11E-124 |
| 5 | g740.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 512 | 555 | 6.54E-8 |
| 16 | g740.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 7 | 29 | - |
| 17 | g740.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 646 | 668 | - |
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 K06842 (semaphorin 6)
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.
