General information for g8948.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Semaphorin-2A.
Parent gene
- The parent gene g8948 is located on chr_2: 34070792..34107159 (+ 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 | g8948 | g8948.t1 | isoform | g8948.t1 | 34070792 | 34107159 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon1 | 34070792 | 34070963 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS1 | 34070792 | 34070963 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon2 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS2 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon3 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS3 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon4 | 34089723 | 34089791 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS4 | 34089723 | 34089791 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon5 | 34090039 | 34090146 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS5 | 34090039 | 34090146 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon6 | 34091233 | 34091370 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS6 | 34091233 | 34091370 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon7 | 34092552 | 34092684 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS7 | 34092552 | 34092684 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon8 | 34093634 | 34093990 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS8 | 34093634 | 34093990 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon9 | 34096840 | 34097068 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS9 | 34096840 | 34097068 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon10 | 34101370 | 34101706 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS10 | 34101370 | 34101706 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon11 | 34103139 | 34103302 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS11 | 34103139 | 34103302 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon12 | 34103706 | 34103858 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS12 | 34103706 | 34103858 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon13 | 34104027 | 34104135 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS13 | 34104027 | 34104135 |
| chr_2 | g8948 | g8948.t1 | exon | g8948.t1.exon14 | 34107082 | 34107159 |
| chr_2 | g8948 | g8948.t1 | cds | g8948.t1.CDS14 | 34107082 | 34107159 |
| chr_2 | g8948 | g8948.t1 | TTS | g8948.t1 | 34107817 | 34107817 |
| chr_2 | g8948 | g8948.t1 | TSS | g8948.t1 | NA | NA |
Sequences
>g8948.t1 Gene=g8948 Length=2187
ATGAAGTTGAATAAGTTGAAAATGTCTTATTTATCGAGTAGTGTCAGTGTGTTGTTCATT
TTCTTATTTCTATTGGATAATACGATCGTTCTTGCCGATTATGAAAATACATTTAGTAGT
TATTTTGAGCAGCAATGCTGTAATGGACCACATCATCTAAGGCATCATAAAGATCATGTA
CGAGAATTCACATGTGGAAAGTTATACTATAGAACATTCCATTTAGATGAAGACAGAGAT
GCGCTTTATGTTGGTGCTATGGATAGAGTGTATAAATTAAACCTTAAAAATATCACACTA
ACAGGATGCGAGAAAGACCACATACTGTTAGATCCAACAGGAAGTGATATAAGTAATTGC
GTATCGAAGGGAAAGAGCCAGCTCTTTGACTGCCGAAATCACATTCGAGTGATACAATCT
ATGGAAAATGGAAATCGTTTATACATCTGCGGAACAAACGCTCATAATCCTAAAGATTAC
GTAATTTATTCAAATCTCACACACTTGCCGAGATCAGAATTTGTTCCAGGAATTGGTTTG
GGAATTGGAAAATGTCCATATGATCCGGTAGATAACTCGACAGCAATTTATGTCGAGCAA
GGAAATCCTGGCAATTTTCCTGCATTGTATTCTGGAACAAACGCAGAATTTACAAAAGCT
GATGCTGTCATTTTTCGTTCAGACATTTACAATCTTACATCAGGACGGAAAGAATTCAAC
TTTAAGCGAACTTTAAAATATGATTCAAAATGGCTTGACAAACCTAATTTCGTGGGATCA
TTTGACATTGGCGAGTATGTTTACTTCTTTTTCCGCGAGACATCTGTCGAGTATATAAAT
TGTGGTAAAGCTGTGTATTCACGTGTTGCACGAGTCTGCAAGAATGACATTGGTGGCAAA
AATATTTTGAGTCAAAATTTTGCAACTTATTTGAAAGCTCGACTTAACTGCAGCATTTCT
GGTGAATTTCCATTCTATTTCAATGAGATTCAATCAGTTTATCAAATTCCAACTGACAAG
ACGAAATTTTATGCAACATTTACCACAAGCACAAATGGTTTAGTTGGATCAGCAGTTTGC
AGTTTTGATATAGGAGAAATTCATGCAGCATTCAATGGAAAATTCAAGGAGCAAGCAAAA
TCAGATTCTGCATGGCTACCAGTTTTAAATTCAAAGGTTCCAGAGCCTCGTCCAGGAACT
TGTGTGAATGACACTTCTAGCCTACCCGACACCGTTCTCAATTTCATTCGTTCACATCCG
CTAATGGATAAAGCCGTTAATCATGAGCACAACAATCCTGTATTTTACAAGCGTGATCTC
GTGTTCACCAAGCTGGTCGTTGACAAAATTTACATAAAAATATTGAATCAAGAGTACAAG
GTATTCTACATTGGCACCAATAACGGTCGCATCTATAAAATTGTTCAATTTATGCAAAAT
GGCGACTCAAAATCTACGCTTCTCGATATATTCGAAGTCGCACAGAACGAGCCGATTCAG
GTGATGCAAATCAGTCAGAAGCGTAAATCACTTTACGTGTCCACAGATCATCGTATCAAG
CAAATTGATTTGGCCATGTGTGCTCGTCGCTACGATAGCTGTTTCCGATGTGTGAAAGAT
CCATATTGTGGATGGGACAGTGACTCCAATTCATGCAAACCATATGAGCTTGGACTTTTG
CAGGACGTTGCTAACGATACAAATGATATATGCGATACAAGTGTTCAAAAGAAGAAAATT
GTCGTCACTTATGGACAAAGTGTGCACTTGGGATGTTTTGTAAAAATTCCAGAAGTTCTC
AAAGATCAACAAGTTTCATGGCATCATTACTCGAAGGATAAGGGACGTTATGAGGTAAAA
TATAGTCCAACAAAATATATCGACACAACAGAACGTGGTCTAGTCGTGGTCTCTGTCAAT
GAGGGTGATGCTGGCCGTTATGATTGCTATTTGGGCGGTTCTTTATTGTGCAGCTATAGC
ATTACTGTTGATGCTCACAGATGTACACCACCGAATAAAGGCAATGACTATCAGAAAATT
TACTCTGACTGGTGTCACGAGTTCGAGAAATACAAATCGGCCATGAAAACGTGGGAGAAG
AAACAAGCTCAATGCTCAGCGAAACAAAACTTTAGTAATCAGCATCCTAATGAAGTATTC
AACAGAAACTCAAACAACAATGTCTGA
>g8948.t1 Gene=g8948 Length=728
MKLNKLKMSYLSSSVSVLFIFLFLLDNTIVLADYENTFSSYFEQQCCNGPHHLRHHKDHV
REFTCGKLYYRTFHLDEDRDALYVGAMDRVYKLNLKNITLTGCEKDHILLDPTGSDISNC
VSKGKSQLFDCRNHIRVIQSMENGNRLYICGTNAHNPKDYVIYSNLTHLPRSEFVPGIGL
GIGKCPYDPVDNSTAIYVEQGNPGNFPALYSGTNAEFTKADAVIFRSDIYNLTSGRKEFN
FKRTLKYDSKWLDKPNFVGSFDIGEYVYFFFRETSVEYINCGKAVYSRVARVCKNDIGGK
NILSQNFATYLKARLNCSISGEFPFYFNEIQSVYQIPTDKTKFYATFTTSTNGLVGSAVC
SFDIGEIHAAFNGKFKEQAKSDSAWLPVLNSKVPEPRPGTCVNDTSSLPDTVLNFIRSHP
LMDKAVNHEHNNPVFYKRDLVFTKLVVDKIYIKILNQEYKVFYIGTNNGRIYKIVQFMQN
GDSKSTLLDIFEVAQNEPIQVMQISQKRKSLYVSTDHRIKQIDLAMCARRYDSCFRCVKD
PYCGWDSDSNSCKPYELGLLQDVANDTNDICDTSVQKKKIVVTYGQSVHLGCFVKIPEVL
KDQQVSWHHYSKDKGRYEVKYSPTKYIDTTERGLVVVSVNEGDAGRYDCYLGGSLLCSYS
ITVDAHRCTPPNKGNDYQKIYSDWCHEFEKYKSAMKTWEKKQAQCSAKQNFSNQHPNEVF
NRNSNNNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g8948.t1 | CDD | cd11238 | Sema_2A | 68 | 525 | 0.0 |
| 8 | g8948.t1 | Gene3D | G3DSA:2.130.10.10 | - | 50 | 528 | 6.9E-150 |
| 10 | g8948.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 529 | 573 | 3.7E-5 |
| 9 | g8948.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 574 | 664 | 1.7E-5 |
| 2 | g8948.t1 | PANTHER | PTHR11036:SF90 | SEMAPHORIN 2B, ISOFORM D-RELATED | 14 | 723 | 0.0 |
| 3 | g8948.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 14 | 723 | 0.0 |
| 1 | g8948.t1 | Pfam | PF01403 | Sema domain | 72 | 506 | 1.7E-132 |
| 12 | g8948.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 32 | - |
| 13 | g8948.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 13 | - |
| 14 | g8948.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 14 | 25 | - |
| 15 | g8948.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 32 | - |
| 11 | g8948.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 33 | 728 | - |
| 20 | g8948.t1 | ProSiteProfiles | PS51004 | Sema domain profile. | 43 | 524 | 117.645 |
| 21 | g8948.t1 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 554 | 662 | 7.595 |
| 18 | g8948.t1 | SMART | SM00630 | sema | 70 | 508 | 6.1E-178 |
| 19 | g8948.t1 | SMART | SM00409 | IG_3c | 577 | 664 | 0.005 |
| 5 | g8948.t1 | SUPERFAMILY | SSF101912 | Sema domain | 58 | 528 | 1.31E-140 |
| 4 | g8948.t1 | SUPERFAMILY | SSF48726 | Immunoglobulin | 577 | 666 | 6.12E-7 |
| 7 | g8948.t1 | SignalP_EUK | SignalP-TM | SignalP-TM | 1 | 32 | - |
| 6 | g8948.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 32 | - |
| 17 | g8948.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 13 | 32 | - |
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 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.
