General information for g6262.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Semaphorin-1A.
Parent gene
- The parent gene g6262 is located on chr_2: 15725594..15738955 (- 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 | g6262 | g6262.t1 | isoform | g6262.t1 | 15663641 | 15731137 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon1 | 15663641 | 15663784 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS1 | 15663641 | 15663784 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon2 | 15663850 | 15664036 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS2 | 15663850 | 15664036 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon3 | 15664103 | 15664367 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS3 | 15664103 | 15664367 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon4 | 15665508 | 15665713 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS4 | 15665508 | 15665713 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon5 | 15665779 | 15665890 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS5 | 15665779 | 15665890 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon6 | 15674335 | 15674478 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS6 | 15674335 | 15674478 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon7 | 15677164 | 15677246 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS7 | 15677164 | 15677246 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon8 | 15677372 | 15677517 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS8 | 15677372 | 15677517 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon9 | 15680418 | 15680498 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS9 | 15680418 | 15680498 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon10 | 15681444 | 15681565 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS10 | 15681444 | 15681565 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon11 | 15681751 | 15681892 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS11 | 15681751 | 15681892 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon12 | 15682082 | 15682170 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS12 | 15682082 | 15682170 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon13 | 15682287 | 15682391 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS13 | 15682287 | 15682391 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon14 | 15687715 | 15687910 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS14 | 15687715 | 15687910 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon15 | 15689338 | 15689446 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS15 | 15689338 | 15689446 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon16 | 15696069 | 15696165 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS16 | 15696069 | 15696165 |
| chr_2 | g6262 | g6262.t1 | exon | g6262.t1.exon17 | 15730948 | 15731137 |
| chr_2 | g6262 | g6262.t1 | cds | g6262.t1.CDS17 | 15730948 | 15731137 |
| chr_2 | g6262 | g6262.t1 | TSS | g6262.t1 | NA | NA |
| chr_2 | g6262 | g6262.t1 | TTS | g6262.t1 | NA | NA |
Sequences
>g6262.t1 Gene=g6262 Length=2418
ATGATGACGTCAGCCAATTCAACATCACCTCCCAGCAAATTGTCTTCGCATGCCAACAAT
TATCAGCGGCATCAGCATAATTATTTCAATAAATTACTCATAATTTTAATTGTTATATTA
ATTAATTGCATTGTTGGAAATTTATGTGCCTGGCAAGACAATGTTCGACCAAAATTATTC
GTTCAATTAGGCGCTGACGATGTTCTCAAATTTCAAGGAAACGACTCAACAATTGATCAT
TTCCGACTGATATTACGAGTTGGTGATAGTTTATTAGTCGGAGGAAGAAACGTTATCTAT
AATCTAAGTATTTTTGACTTATCAGAGCATAACAGAGTGCTCTGGTTTTCAGCAGAAGAT
GATATTAAGATGTGTTTAGTAAAAGGAAAGGACGAGGAATCATGTCAGAATTATATTCGC
ATTTTAACAATCACAACACCGGGAATTCTGTTGGCATGTGGAACAAATTCCTATCGGCCA
ATGTGTCACTTTTACAATATCACCGGCAGTAAATATCACATTGAAAAGACGAAGCCTGGT
CAAGCATTATGTCCTTATGGACCGAAACACAATTCAACATCCGTATTTGTTGATAATGAT
CTATACACAGGAACTGATGCTGATTTCAGTGGCAACGACCCAATCATTTATCGTGAGCCA
TTACAGACTGACCAGTTTGATAGTCTGAGTTTAAATGCACCCAATTTCGTGGGATCATTT
ACAGCGGGCGATTTTGTGTATTTCTTCTTCCGTGAAACAGCTGTTGAGTTTATCAACTGC
GGCAAGTCTGTATACAGCCGTATTGCACGTGTGTGTAAATGGGATAAAGGTGGACCTCAT
CGTTTTCGTAATCGTTGGACAACTTTCCTCAAATCACGACTCAATTGCTCCATTCCTGGA
GATTTTCCATTCTATTTTAATGAAATTCAATCAAATAGTGAACTCGTGGAGGGAACTTAC
GGGAACACAAATGCTCGTTTAATTTATGGTGTATTCACTACATCGCACAATGCCATTGCA
GGATCAGCCATCTGTGCATTTTCTCTGCAGGAAATTTCTGATACATTTGAGGGCAATTTT
AAGGAGCAATCTAGTATTCATTCGACATGGAAGCCAGTAGAAAAGTCAAAGATTCCAGAA
CCGAGACCGGGCTCTTGTCACAATGATACAAGAGCATTGCCTGAAGCGACACTCACGTTC
ATTAAAACACATTCATTGATGGACGAAAATGTGCCAGCATACTTTGGACTTCCAATTTTA
ACAAGAGTGGGCACACCGTACCGTTTCACACAAATTGCAGTTGATCCACAAATAAAAACG
CCAGGAGGCAGAACATACGATGTGATATTCGTCGGCACAGATCATGGAAAAGTGCTGAAA
ACAATAAATGCTGCATCAGCAAACGATTCTAGCAAAGTGACATCAGTGGTTATTGAAGAA
TTGGATGTTCTTTCCAAACCTGAACCAATTAGAAATTTGAAGATTGTCCGGACAATGCAA
TATGAAAATCCAAAAGATGGCAATTATGACGATGGAAAATTGATCATTGTTACTGACAGT
CAAATTCTTGGAATTCCTTTACATCGATGTAATAGTGAGAAAATCAATAGCTGCAGTGAT
TGTGTCGCACTTCAAGATCCATATTGCGCTTGGGACAAGATTGCTGGAAAATGTCGTTCA
CATGGAGCACCACGATGGATTGATGAGACTTACTTCTACTCAGAAGTATCTACAGGTCAA
CATTCGGCGTGTCCATCGGGAAAATCAAAAGACCCGAATGTCGAGTCGAAAGGTTACCGA
GATGACTTTGACATGAGAATGGGCAAGGATGGTGAATTAAGTGGAACAATGCAAGACAAA
AGCTATGACGGCATCAATGGACCACAAATTCGTGCTGATGCTATAAATGCACAATACACA
GTAGAAACAGTTGTTATGGCAGTTCTCGCTGCTGCTATTTTTGCACTGCTTGTGGGTTTC
ATCACAGGCTACTTTTGCGGAAGACGTTGCCATAAGGATGAGGATGACAATTTGCCTTAT
CCGGACACTGAATACGAGTATTTTGAGCAACGATCGAATATCAATCGCCTACAAACTGAA
CCCAAATTATTGCCACAAGTTGAAGAAGTTACTTATGCTGAACCTGTTCTGCTGCCTCAA
CCACCCAATTCTAATAAAATGCATCAACCGCCTATGGGATCGCCTAAAAGTACATTAAGA
AAGCCAATGATGCCACATCATCATGGTGGTGTTAATTCAGAAACTTTATTCCAGTTCCAA
CCAGATGGTTATAATCCACCACGTGATATGAATTATCGTGGTCGTGACAACTTTGGCACA
CTGCGATCACACCAGGGCGACAATTACAGACGCGATGGCTTCTCAACGACAAGAAGCGTA
AAGAAAGTTTATCTATGA
>g6262.t1 Gene=g6262 Length=805
MMTSANSTSPPSKLSSHANNYQRHQHNYFNKLLIILIVILINCIVGNLCAWQDNVRPKLF
VQLGADDVLKFQGNDSTIDHFRLILRVGDSLLVGGRNVIYNLSIFDLSEHNRVLWFSAED
DIKMCLVKGKDEESCQNYIRILTITTPGILLACGTNSYRPMCHFYNITGSKYHIEKTKPG
QALCPYGPKHNSTSVFVDNDLYTGTDADFSGNDPIIYREPLQTDQFDSLSLNAPNFVGSF
TAGDFVYFFFRETAVEFINCGKSVYSRIARVCKWDKGGPHRFRNRWTTFLKSRLNCSIPG
DFPFYFNEIQSNSELVEGTYGNTNARLIYGVFTTSHNAIAGSAICAFSLQEISDTFEGNF
KEQSSIHSTWKPVEKSKIPEPRPGSCHNDTRALPEATLTFIKTHSLMDENVPAYFGLPIL
TRVGTPYRFTQIAVDPQIKTPGGRTYDVIFVGTDHGKVLKTINAASANDSSKVTSVVIEE
LDVLSKPEPIRNLKIVRTMQYENPKDGNYDDGKLIIVTDSQILGIPLHRCNSEKINSCSD
CVALQDPYCAWDKIAGKCRSHGAPRWIDETYFYSEVSTGQHSACPSGKSKDPNVESKGYR
DDFDMRMGKDGELSGTMQDKSYDGINGPQIRADAINAQYTVETVVMAVLAAAIFALLVGF
ITGYFCGRRCHKDEDDNLPYPDTEYEYFEQRSNINRLQTEPKLLPQVEEVTYAEPVLLPQ
PPNSNKMHQPPMGSPKSTLRKPMMPHHHGGVNSETLFQFQPDGYNPPRDMNYRGRDNFGT
LRSHQGDNYRRDGFSTTRSVKKVYL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 14 | g6262.t1 | CDD | cd11237 | Sema_1A | 76 | 530 | 0.0 |
| 7 | g6262.t1 | Gene3D | G3DSA:2.130.10.10 | - | 61 | 531 | 1.5E-158 |
| 8 | g6262.t1 | Gene3D | G3DSA:3.30.1680.10 | - | 532 | 589 | 2.7E-12 |
| 19 | g6262.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 721 | 740 | - |
| 3 | g6262.t1 | PANTHER | PTHR11036 | SEMAPHORIN | 67 | 731 | 1.2E-216 |
| 4 | g6262.t1 | PANTHER | PTHR11036:SF127 | SEMAPHORIN-1A | 67 | 731 | 1.2E-216 |
| 1 | g6262.t1 | Pfam | PF01403 | Sema domain | 88 | 496 | 7.8E-130 |
| 2 | g6262.t1 | Pfam | PF01437 | Plexin repeat | 534 | 569 | 7.3E-6 |
| 9 | g6262.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 31 | - |
| 12 | g6262.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 32 | 51 | - |
| 11 | g6262.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 52 | 643 | - |
| 13 | g6262.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 644 | 666 | - |
| 10 | g6262.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 667 | 805 | - |
| 20 | g6262.t1 | ProSiteProfiles | PS51004 | Sema domain profile. | 60 | 527 | 111.75 |
| 17 | g6262.t1 | SMART | SM00630 | sema | 81 | 499 | 1.7E-169 |
| 18 | g6262.t1 | SMART | SM00423 | psinew7 | 529 | 585 | 1.0E-8 |
| 6 | g6262.t1 | SUPERFAMILY | SSF101912 | Sema domain | 60 | 531 | 5.76E-143 |
| 5 | g6262.t1 | SUPERFAMILY | SSF103575 | Plexin repeat | 534 | 574 | 7.06E-9 |
| 15 | g6262.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 29 | 51 | - |
| 16 | g6262.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 644 | 666 | - |
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.
