General information for g8948.t2
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.t2 | isoform | g8948.t2 | 34062712 | 34107159 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon1 | 34062712 | 34062823 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS1 | 34062712 | 34062823 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon2 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS2 | 34078725 | 34078812 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon3 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS3 | 34082200 | 34082251 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon4 | 34089723 | 34089791 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS4 | 34089723 | 34089791 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon5 | 34090039 | 34090146 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS5 | 34090039 | 34090146 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon6 | 34091233 | 34091370 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS6 | 34091233 | 34091370 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon7 | 34092552 | 34092684 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS7 | 34092552 | 34092684 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon8 | 34093634 | 34093990 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS8 | 34093634 | 34093990 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon9 | 34096840 | 34097068 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS9 | 34096840 | 34097068 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon10 | 34101370 | 34101706 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS10 | 34101370 | 34101706 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon11 | 34103139 | 34103302 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS11 | 34103139 | 34103302 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon12 | 34103706 | 34103858 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS12 | 34103706 | 34103858 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon13 | 34104027 | 34104135 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS13 | 34104027 | 34104135 |
| chr_2 | g8948 | g8948.t2 | exon | g8948.t2.exon14 | 34107082 | 34107159 |
| chr_2 | g8948 | g8948.t2 | cds | g8948.t2.CDS14 | 34107082 | 34107159 |
| chr_2 | g8948 | g8948.t2 | TTS | g8948.t2 | 34107817 | 34107817 |
| chr_2 | g8948 | g8948.t2 | TSS | g8948.t2 | NA | NA |
Sequences
>g8948.t2 Gene=g8948 Length=2127
ATGTTTAAATTAACTAAAGTAAACATCACTTGGTTGCTTTTAAGCATTCTTGTTTTACTC
CTGCCATCATCGACATGTTCATCGAATGTTATGCTGGAGGAGCTTTCACCAGATCATGTA
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.t2 Gene=g8948 Length=708
MFKLTKVNITWLLLSILVLLLPSSTCSSNVMLEELSPDHVREFTCGKLYYRTFHLDEDRD
ALYVGAMDRVYKLNLKNITLTGCEKDHILLDPTGSDISNCVSKGKSQLFDCRNHIRVIQS
MENGNRLYICGTNAHNPKDYVIYSNLTHLPRSEFVPGIGLGIGKCPYDPVDNSTAIYVEQ
GNPGNFPALYSGTNAEFTKADAVIFRSDIYNLTSGRKEFNFKRTLKYDSKWLDKPNFVGS
FDIGEYVYFFFRETSVEYINCGKAVYSRVARVCKNDIGGKNILSQNFATYLKARLNCSIS
GEFPFYFNEIQSVYQIPTDKTKFYATFTTSTNGLVGSAVCSFDIGEIHAAFNGKFKEQAK
SDSAWLPVLNSKVPEPRPGTCVNDTSSLPDTVLNFIRSHPLMDKAVNHEHNNPVFYKRDL
VFTKLVVDKIYIKILNQEYKVFYIGTNNGRIYKIVQFMQNGDSKSTLLDIFEVAQNEPIQ
VMQISQKRKSLYVSTDHRIKQIDLAMCARRYDSCFRCVKDPYCGWDSDSNSCKPYELGLL
QDVANDTNDICDTSVQKKKIVVTYGQSVHLGCFVKIPEVLKDQQVSWHHYSKDKGRYEVK
YSPTKYIDTTERGLVVVSVNEGDAGRYDCYLGGSLLCSYSITVDAHRCTPPNKGNDYQKI
YSDWCHEFEKYKSAMKTWEKKQAQCSAKQNFSNQHPNEVFNRNSNNNV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g8948.t2 | CDD | cd11238 | Sema_2A | 48 | 505 | 0.0 |
| 7 | g8948.t2 | Gene3D | G3DSA:2.130.10.10 | - | 28 | 508 | 8.3E-150 |
| 9 | g8948.t2 | Gene3D | G3DSA:3.30.1680.10 | - | 509 | 553 | 3.6E-5 |
| 8 | g8948.t2 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 554 | 644 | 1.6E-5 |
| 2 | g8948.t2 | PANTHER | PTHR11036:SF90 | SEMAPHORIN 2B, ISOFORM D-RELATED | 27 | 703 | 0.0 |
| 3 | g8948.t2 | PANTHER | PTHR11036 | SEMAPHORIN | 27 | 703 | 0.0 |
| 1 | g8948.t2 | Pfam | PF01403 | Sema domain | 52 | 486 | 1.6E-132 |
| 11 | g8948.t2 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 12 | g8948.t2 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 9 | - |
| 13 | g8948.t2 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 10 | 21 | - |
| 14 | g8948.t2 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 22 | 26 | - |
| 10 | g8948.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 708 | - |
| 18 | g8948.t2 | ProSiteProfiles | PS51004 | Sema domain profile. | 27 | 504 | 118.347 |
| 19 | g8948.t2 | ProSiteProfiles | PS50835 | Ig-like domain profile. | 534 | 642 | 7.595 |
| 16 | g8948.t2 | SMART | SM00630 | sema | 50 | 488 | 6.1E-178 |
| 17 | g8948.t2 | SMART | SM00409 | IG_3c | 557 | 644 | 0.005 |
| 5 | g8948.t2 | SUPERFAMILY | SSF101912 | Sema domain | 16 | 508 | 3.14E-142 |
| 4 | g8948.t2 | SUPERFAMILY | SSF48726 | Immunoglobulin | 557 | 646 | 5.97E-7 |
| 6 | g8948.t2 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 27 | - |
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.
