General information for g8950.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Semaphorin-2A.
Parent gene
- The parent gene g8950 is located on chr_2: 34140368..34144294 (- 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 | g8950 | g8950.t1 | TTS | g8950.t1 | 34140362 | 34140362 |
| chr_2 | g8950 | g8950.t1 | isoform | g8950.t1 | 34140368 | 34144294 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon1 | 34140368 | 34140421 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS1 | 34140368 | 34140421 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon2 | 34140607 | 34140715 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS2 | 34140607 | 34140715 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon3 | 34140773 | 34140925 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS3 | 34140773 | 34140925 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon4 | 34141024 | 34141187 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS4 | 34141024 | 34141187 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon5 | 34141581 | 34141917 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS5 | 34141581 | 34141917 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon6 | 34141999 | 34142584 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS6 | 34141999 | 34142584 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon7 | 34142680 | 34142812 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS7 | 34142680 | 34142812 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon8 | 34142875 | 34143012 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS8 | 34142875 | 34143012 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon9 | 34143511 | 34143615 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS9 | 34143511 | 34143615 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon10 | 34143772 | 34143840 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS10 | 34143772 | 34143840 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon11 | 34143914 | 34143965 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS11 | 34143914 | 34143965 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon12 | 34144030 | 34144117 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS12 | 34144030 | 34144117 |
| chr_2 | g8950 | g8950.t1 | exon | g8950.t1.exon13 | 34144261 | 34144294 |
| chr_2 | g8950 | g8950.t1 | cds | g8950.t1.CDS13 | 34144261 | 34144294 |
| chr_2 | g8950 | g8950.t1 | TSS | g8950.t1 | NA | NA |
Sequences
>g8950.t1 Gene=g8950 Length=2022
ATGAATCATATTTTTTGGCACGCGATTAAAACACACCATGTGAGGGAATTCACATGTGGG
AAGCTGTATTACAGAACAGTTTTGCTCCAAGAGCATAATGAGGCACTTTTTGTTGGTGCT
ATGGATCGGGTGATGAAACTTCATTTAGATGACATAAGTAGAACAAATTGTGAACGAGAT
CATATACTAATGGAGCCTACATCAAGCGACGTTCTCAACTGCGTTTCAAAAGGAAAAAGC
CAGCTCTTTGATTGTCGCAATCACATACGCGTGCTACAGCCTATGGAAGGAAATCGACTC
TATATATGTGGTACTTACGCTCACAATCCAAAGGATTATATCATCTTTACAAATCTTACA
CATTTACCAAGATCAGAGCTTTTGCCAGGTATTGGTTATGGAATTGGCAAGTGCCCTTAC
GATCCGCTTGATAATTCAACCGCTATTTATGTCGAAAAGGGTAATCCAGGCAATTTTGCA
GCATTGTATTCTGGAACAAATGCTGAATTTACAAAAGCTGATTCAGTGATTTTCCGTGCA
GACATTTATAACATGACAACTGGCCGAAAGGAGTATAATTTTAAGCGTACACTGAAATAC
GATTCGAAATGGCTCGACAAACCTAATTTTGTTGGATCATTTGACATTGGCGAGTATGTT
TACTTCTTTTTCCGCGAGACAGCTGTCGAGTATATAAATTGTGGTAAAGCTGTGTATTCA
CGTGTTGCACGAGTCTGCAAGAATGACATTGGTGGCAAAAATATTTTGAGTCAAAATTTT
GCAACTTATTTGAAAGCTCGACTTAACTGCAGCATTTCTGGTGAATTTCCATTCTATTTC
AATGAGATTCAATCAGTTTATCAAATTCCAACTGACAAGACGAAATTTTATGCAACATTT
ACCACAAGCACAAATGGTTTAGTTGGATCAGCAGTTTGCAGTTTTGATATAGGTGAAATT
CATGCAACTTTCAAGGGAAAATTCAAGGAGCAAGCAAAATCAGATTCTGCATGGCTACCA
GTTTTAAATTCAAAAGTTCCAGAGCCTCGTCCTGGCACATGCGTTTCCGACACCTCGAAT
CTACCCGATACTGTTCTCAATTTCATTCGCTCGCACCCACTAATGGACAAACCAGTCAAT
CATGAGCACAACAATCCTGTATTTTATAAGCGCGATTTGGTATTCACAAAATTAGCTGTT
GACAAAATACGCAATCAAATAACAAATCATGAATTTAAAGTTTATTATGTTGGCACAAAC
AATGGTCGAATCTATAAAATTGTACAATTTATGCGTGACGGTGAGACCAAATCGAAGTTG
CTGGATATTTTTGAAATTGCCAAAAATGAAGCAATTCAAGTTATTGAGATCAGTCAGAAG
CATAAATCACTTTATGTAACAACTGATCATCGTATTAAACAGATTGCTTTACAAATGTGC
AGTCATCGATATGACAGTTGCTTTAGATGTGTGAAAGATCCTTATTGTGGTTGGGATACT
AATGCAAATGCTTGTAAACCGTATGAGCTTGGATTATTACAGGATGTTGCCAATGAGACA
AACGATATTTGTGACTCAAGTGTGTCAAAAAATAAAATCATTGTAACATATGGTCAGAGT
ATACATTTGGGATGTTTTGAGACAGTTCCGGAGATTTTAAGAGATCAACAAGTGGTATGG
TATCATCACTCGAAAGATAATGGACGATATGAAATCAGATACAATGCCCACAAACACATC
GAAACAACAGAACGAGGATTAGTGATTGTGGCAGCACACGAGAGCGATAGTGGTCGTTAT
GATTGTCATTTAGGTGGATCACTATTGTGTAGTTACATCATAACAGTTGATGCACATAGA
TGTACCGCACCAAATAAGAGCAACGATTATCAAAAAATTTATGCTGACTGGTGCCATGAA
TTCGAAAAATACAAATCCGCAATGAAATTGTGGGAAAAGCGACAATCGCAATGTTCAACC
CCTCAGAATTCCAGCAGCAATAATGAAATCCCAAAGAACTGA
>g8950.t1 Gene=g8950 Length=673
MNHIFWHAIKTHHVREFTCGKLYYRTVLLQEHNEALFVGAMDRVMKLHLDDISRTNCERD
HILMEPTSSDVLNCVSKGKSQLFDCRNHIRVLQPMEGNRLYICGTYAHNPKDYIIFTNLT
HLPRSELLPGIGYGIGKCPYDPLDNSTAIYVEKGNPGNFAALYSGTNAEFTKADSVIFRA
DIYNMTTGRKEYNFKRTLKYDSKWLDKPNFVGSFDIGEYVYFFFRETAVEYINCGKAVYS
RVARVCKNDIGGKNILSQNFATYLKARLNCSISGEFPFYFNEIQSVYQIPTDKTKFYATF
TTSTNGLVGSAVCSFDIGEIHATFKGKFKEQAKSDSAWLPVLNSKVPEPRPGTCVSDTSN
LPDTVLNFIRSHPLMDKPVNHEHNNPVFYKRDLVFTKLAVDKIRNQITNHEFKVYYVGTN
NGRIYKIVQFMRDGETKSKLLDIFEIAKNEAIQVIEISQKHKSLYVTTDHRIKQIALQMC
SHRYDSCFRCVKDPYCGWDTNANACKPYELGLLQDVANETNDICDSSVSKNKIIVTYGQS
IHLGCFETVPEILRDQQVVWYHHSKDNGRYEIRYNAHKHIETTERGLVIVAAHESDSGRY
DCHLGGSLLCSYIITVDAHRCTAPNKSNDYQKIYADWCHEFEKYKSAMKLWEKRQSQCST
PQNSSSNNEIPKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g8950.t1 | CDD | cd11238 | Sema_2A | 22 | 477 | 0.0000000 |
| 8 | g8950.t1 | Gene3D | G3DSA:2.130.10.10 | - | 3 | 481 | 0.0000000 |
| 10 | g8950.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 482 | 526 | 0.0000029 |
| 9 | g8950.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 527 | 616 | 0.0000021 |
| 2 | g8950.t1 | PANTHER | PTHR11036:SF90 | SEMAPHORIN 2B, ISOFORM D-RELATED | 8 | 668 | 0.0000000 |
| 3 | g8950.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 8 | 668 | 0.0000000 |
| 1 | g8950.t1 | Pfam | PF01403 | Sema domain | 26 | 458 | 0.0000000 |
| 11 | g8950.t1 | ProSiteProfiles | PS51004 | Sema domain profile. | 1 | 477 | 114.5030000 |
| 12 | g8950.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 538 | 602 | 7.3220000 |
| 7 | g8950.t1 | SMART | SM00630 | sema | 24 | 461 | 0.0000000 |
| 6 | g8950.t1 | SUPERFAMILY | SSF101912 | Sema domain | 3 | 477 | 0.0000000 |
| 4 | g8950.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 482 | 509 | 0.0000324 |
| 5 | g8950.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 532 | 617 | 0.0000001 |
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 K06840 (semaphorin 3)
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.
