General information for g1466.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Neurexin-3-beta.
Parent gene
- The parent gene g1466 is located on chr_3: 11070291..11086453 (- 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 | g1466 | g1466.t1 | isoform | g1466.t1 | 11070291 | 11086453 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon1 | 11070291 | 11071159 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS1 | 11070291 | 11071159 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon2 | 11071311 | 11071544 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS2 | 11071311 | 11071544 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon3 | 11071610 | 11071913 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS3 | 11071610 | 11071913 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon4 | 11082392 | 11082633 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS4 | 11082392 | 11082633 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon5 | 11082732 | 11082903 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS5 | 11082732 | 11082903 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon6 | 11084542 | 11084720 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS6 | 11084542 | 11084720 |
| chr_3 | g1466 | g1466.t1 | exon | g1466.t1.exon7 | 11086450 | 11086453 |
| chr_3 | g1466 | g1466.t1 | cds | g1466.t1.CDS7 | 11086450 | 11086453 |
| chr_3 | g1466 | g1466.t1 | TSS | g1466.t1 | NA | NA |
| chr_3 | g1466 | g1466.t1 | TTS | g1466.t1 | NA | NA |
Sequences
>g1466.t1 Gene=g1466 Length=2004
ATGGAATCAGTGTCATATGAATTTGGTGCTGGTCGTGGTCTTATACAATATCAATTTCCA
CCTGGAAATCAGCCAGACACTGAAGAAGACAACATTGCTCTTGGCTTTATAACACTCAAA
ACTGATGCCATACTGCTACGAATTGAAAGTTCAAATACCCAGGATTATTTTGAATTGGAA
ATTGTGGAAGGAAATGTTTTTGCTGTTTTCAATGTTGGCTCACAAGACTTGCCATTGGGC
GAGATTGGTGTAAAAGTGAACGATAACAATTATCATGTCGTACGATTTACACGACGTGGT
GGTAATGCTACCTTACAGATCGATGATTACAACGTGCAAAATCTTCACGCTCAAGGTCAC
ATATCAACTGTATTCAATTCAATGAGTAACATTCAAGTTGGCGGCAAGGTTCCAAAAGGC
GCAAGCCGTTCACGCATTGAACGAGCATTTGCTGGTGTAATTGCAGGACTTTCCATCAAT
CGTCTTCGAATTCTCGATTTGGCAGCTGAACGTGATCCACAAATTACAATTCGCGGGGAT
GTTCAATTGGTAACTGGCGTATTAGATAGAAATGACCTACATCACAGAATGCAGCAGACA
CCACCAAGTGGTTATCCAGGTGTTATGGATGACTTGATTTTTTCGGGTGCTGGTTCAGGT
TGTCGTGGTGATGATGAGGATGAATGTATGCCACCATTTGAAAATGGCAGTGGTGATGAC
TTGATAACTCCCGTCTATGTTCCACCAACTAAGCAGACAGTCACACAAAATAAAACAAAA
CCAAACAAAAGTGAAAACGAGAAATTATGTGATGATGAAGATTGTCTGCATGGGTCGGGT
TCAGGTGAAGTCACTGACTCATATTCTACACCATCTGTTACAATGCGAGTTGATTCAAAA
GACACGAGTCCTGATGTCTCTCCACATACGACAATTGATGATAAACGAACTGACACGACA
ATGCCAGACACTACTCAACCCGATGAAGAAACTATTGGCTCTGCAGGCACAACAGGATTA
CAAGAAACAACTCATCCACATTCACCATCATCTTTTGGCACAAGTACAACACAATTTATT
AGTTCAACATCACATGGCACAAGCAGTTATGGTACAAGCACAAGAATTATTGAAGAATCA
ACAAGCACAAGTGCAGGAACAACAACAACTACAACAACAAGAGGCACAACAGTTTATATT
CCACCACAAACAGAAACAACAATTCCGTATAAAGAAACTTATCCACCTGAACCAAGCACA
ACCGAGGATGAAAGTAATAATGAAATTATTCCACCACATCAAGAAGAACCAACAGAATAT
GATGATAATATTTATGAACAACCAATACCTGAACCTGAAACTGAAGCTCCACCATTACTG
CCACCGATTTACAATAAACCAAATCGTATTGATCGTATTGATAATCATAATGGTGCAGGT
CATCGTGATCCATCAATATTCAGAGAGCAACCAACAAGAATACCACCAAAGAATAAAAAT
CATGGACGAATAAATTCTGAAGCTGAAGAAAGAACAGCAATGATAATTGGAATTGTTGCT
GGTGCATTAATTGCTGTAATTCTTGTCATACTTTTGGTCTTATGGATTAAATCAAATGGC
GATAGATCATATAAAATGGAACATGATTTAAAATATGGCCATGGTGCAAATGCTGCACTT
TTAGGTCATAATTCAGGTCATCAATCGAACGCACATCATGGAGTTGGTAGTCATCATGGT
AATGGAAGTGGCCAACATCATAGTAGCAGCAGTAATCAACAACATCATCAACATAATCAG
CATCATAGTTCATCGTCATATCAACATGGAAATGGTTACAATCATGGGTCAGGCTATGAT
GCCAGTGGTGAAAGTCCAAATGGCCTAAATGGTTCATTAAGGCAGCAACAGAGTAGTCAT
TATGATCGAAATGGCATGAGTGCTGGTCTCGTGCAGCCGAAAGCAAAACGTAATTCAAAA
GATATCAAAGAATGGTATGTGTAA
>g1466.t1 Gene=g1466 Length=667
MESVSYEFGAGRGLIQYQFPPGNQPDTEEDNIALGFITLKTDAILLRIESSNTQDYFELE
IVEGNVFAVFNVGSQDLPLGEIGVKVNDNNYHVVRFTRRGGNATLQIDDYNVQNLHAQGH
ISTVFNSMSNIQVGGKVPKGASRSRIERAFAGVIAGLSINRLRILDLAAERDPQITIRGD
VQLVTGVLDRNDLHHRMQQTPPSGYPGVMDDLIFSGAGSGCRGDDEDECMPPFENGSGDD
LITPVYVPPTKQTVTQNKTKPNKSENEKLCDDEDCLHGSGSGEVTDSYSTPSVTMRVDSK
DTSPDVSPHTTIDDKRTDTTMPDTTQPDEETIGSAGTTGLQETTHPHSPSSFGTSTTQFI
SSTSHGTSSYGTSTRIIEESTSTSAGTTTTTTTRGTTVYIPPQTETTIPYKETYPPEPST
TEDESNNEIIPPHQEEPTEYDDNIYEQPIPEPETEAPPLLPPIYNKPNRIDRIDNHNGAG
HRDPSIFREQPTRIPPKNKNHGRINSEAEERTAMIIGIVAGALIAVILVILLVLWIKSNG
DRSYKMEHDLKYGHGANAALLGHNSGHQSNAHHGVGSHHGNGSGQHHSSSSNQQHHQHNQ
HHSSSSYQHGNGYNHGSGYDASGESPNGLNGSLRQQQSSHYDRNGMSAGLVQPKAKRNSK
DIKEWYV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1466.t1 | CDD | cd00110 | LamG | 5 | 160 | 7.25621E-22 |
| 5 | g1466.t1 | Gene3D | G3DSA:2.60.120.200 | - | 1 | 189 | 6.7E-49 |
| 16 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 249 | 331 | - |
| 13 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 261 | 279 | - |
| 12 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 282 | 306 | - |
| 14 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 307 | 323 | - |
| 15 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 415 | 434 | - |
| 19 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 476 | 505 | - |
| 18 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 569 | 607 | - |
| 17 | g1466.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 646 | 667 | - |
| 2 | g1466.t1 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 19 | 393 | 8.4E-71 |
| 3 | g1466.t1 | PANTHER | PTHR15036:SF68 | NEUREXIN 1, ISOFORM F | 19 | 393 | 8.4E-71 |
| 1 | g1466.t1 | Pfam | PF02210 | Laminin G domain | 36 | 160 | 1.9E-19 |
| 7 | g1466.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 512 | - |
| 8 | g1466.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 513 | 536 | - |
| 6 | g1466.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 537 | 667 | - |
| 20 | g1466.t1 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 1 | 221 | 23.073 |
| 11 | g1466.t1 | SMART | SM00282 | LamG_3 | 28 | 162 | 3.6E-21 |
| 4 | g1466.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 4 | 160 | 5.77E-27 |
| 10 | g1466.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 514 | 536 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
KEGG
Orthology
- This transcript has been annotated with K07377 (neurexin)
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. There were no conditions that were differentially expressed