General information for g1466.t2
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.t2 | isoform | g1466.t2 | 11070291 | 11086453 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon1 | 11070291 | 11071159 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS1 | 11070291 | 11071159 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon2 | 11071311 | 11071544 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS2 | 11071311 | 11071544 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon3 | 11071610 | 11071913 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS3 | 11071610 | 11071913 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon4 | 11082440 | 11082633 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS4 | 11082440 | 11082633 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon5 | 11082732 | 11082903 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS5 | 11082732 | 11082903 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon6 | 11084542 | 11084720 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS6 | 11084542 | 11084720 |
| chr_3 | g1466 | g1466.t2 | exon | g1466.t2.exon7 | 11086450 | 11086453 |
| chr_3 | g1466 | g1466.t2 | cds | g1466.t2.CDS7 | 11086450 | 11086453 |
| chr_3 | g1466 | g1466.t2 | TSS | g1466.t2 | NA | NA |
| chr_3 | g1466 | g1466.t2 | TTS | g1466.t2 | NA | NA |
Sequences
>g1466.t2 Gene=g1466 Length=1956
ATGGAATCAGTGTCATATGAATTTGGTGCTGGTCGTGGTCTTATACAATATCAATTTCCA
CCTGGAAATCAGCCAGACACTGAAGAAGACAACATTGCTCTTGGCTTTATAACACTCAAA
ACTGATGCCATACTGCTACGAATTGAAAGTTCAAATACCCAGGATTATTTTGAATTGGAA
ATTGTGGAAGGAAATGTTTTTGCTGTTTTCAATGTTGGCTCACAAGACTTGCCATTGGGC
GAGATTGGTGTAAAAGTGAACGATAACAATTATCATGTCGTACGATTTACACGACGTGGT
GGTAATGCTACCTTACAGATCGATGATTACAACGTGCAAAATCTTCACGCTCAAGGTCAC
ATATCAACTGTATTCAATTCAATGAGTAACATTCAAGTTGGCGGCAAGGTTCCAAAAGGC
GCAAGCCGTTCACGCATTGAACGAGCATTTGCTGGTGTAATTGCAGGACTTTCCATCAAT
CGTCTTCGAATTCTCGATTTGGCAGCTGAACGTGATCCACAAATTACAATTCGCGGGGAT
GTTCAATTGACACCACCAAGTGGTTATCCAGGTGTTATGGATGACTTGATTTTTTCGGGT
GCTGGTTCAGGTTGTCGTGGTGATGATGAGGATGAATGTATGCCACCATTTGAAAATGGC
AGTGGTGATGACTTGATAACTCCCGTCTATGTTCCACCAACTAAGCAGACAGTCACACAA
AATAAAACAAAACCAAACAAAAGTGAAAACGAGAAATTATGTGATGATGAAGATTGTCTG
CATGGGTCGGGTTCAGGTGAAGTCACTGACTCATATTCTACACCATCTGTTACAATGCGA
GTTGATTCAAAAGACACGAGTCCTGATGTCTCTCCACATACGACAATTGATGATAAACGA
ACTGACACGACAATGCCAGACACTACTCAACCCGATGAAGAAACTATTGGCTCTGCAGGC
ACAACAGGATTACAAGAAACAACTCATCCACATTCACCATCATCTTTTGGCACAAGTACA
ACACAATTTATTAGTTCAACATCACATGGCACAAGCAGTTATGGTACAAGCACAAGAATT
ATTGAAGAATCAACAAGCACAAGTGCAGGAACAACAACAACTACAACAACAAGAGGCACA
ACAGTTTATATTCCACCACAAACAGAAACAACAATTCCGTATAAAGAAACTTATCCACCT
GAACCAAGCACAACCGAGGATGAAAGTAATAATGAAATTATTCCACCACATCAAGAAGAA
CCAACAGAATATGATGATAATATTTATGAACAACCAATACCTGAACCTGAAACTGAAGCT
CCACCATTACTGCCACCGATTTACAATAAACCAAATCGTATTGATCGTATTGATAATCAT
AATGGTGCAGGTCATCGTGATCCATCAATATTCAGAGAGCAACCAACAAGAATACCACCA
AAGAATAAAAATCATGGACGAATAAATTCTGAAGCTGAAGAAAGAACAGCAATGATAATT
GGAATTGTTGCTGGTGCATTAATTGCTGTAATTCTTGTCATACTTTTGGTCTTATGGATT
AAATCAAATGGCGATAGATCATATAAAATGGAACATGATTTAAAATATGGCCATGGTGCA
AATGCTGCACTTTTAGGTCATAATTCAGGTCATCAATCGAACGCACATCATGGAGTTGGT
AGTCATCATGGTAATGGAAGTGGCCAACATCATAGTAGCAGCAGTAATCAACAACATCAT
CAACATAATCAGCATCATAGTTCATCGTCATATCAACATGGAAATGGTTACAATCATGGG
TCAGGCTATGATGCCAGTGGTGAAAGTCCAAATGGCCTAAATGGTTCATTAAGGCAGCAA
CAGAGTAGTCATTATGATCGAAATGGCATGAGTGCTGGTCTCGTGCAGCCGAAAGCAAAA
CGTAATTCAAAAGATATCAAAGAATGGTATGTGTAA
>g1466.t2 Gene=g1466 Length=651
MESVSYEFGAGRGLIQYQFPPGNQPDTEEDNIALGFITLKTDAILLRIESSNTQDYFELE
IVEGNVFAVFNVGSQDLPLGEIGVKVNDNNYHVVRFTRRGGNATLQIDDYNVQNLHAQGH
ISTVFNSMSNIQVGGKVPKGASRSRIERAFAGVIAGLSINRLRILDLAAERDPQITIRGD
VQLTPPSGYPGVMDDLIFSGAGSGCRGDDEDECMPPFENGSGDDLITPVYVPPTKQTVTQ
NKTKPNKSENEKLCDDEDCLHGSGSGEVTDSYSTPSVTMRVDSKDTSPDVSPHTTIDDKR
TDTTMPDTTQPDEETIGSAGTTGLQETTHPHSPSSFGTSTTQFISSTSHGTSSYGTSTRI
IEESTSTSAGTTTTTTTRGTTVYIPPQTETTIPYKETYPPEPSTTEDESNNEIIPPHQEE
PTEYDDNIYEQPIPEPETEAPPLLPPIYNKPNRIDRIDNHNGAGHRDPSIFREQPTRIPP
KNKNHGRINSEAEERTAMIIGIVAGALIAVILVILLVLWIKSNGDRSYKMEHDLKYGHGA
NAALLGHNSGHQSNAHHGVGSHHGNGSGQHHSSSSNQQHHQHNQHHSSSSYQHGNGYNHG
SGYDASGESPNGLNGSLRQQQSSHYDRNGMSAGLVQPKAKRNSKDIKEWYV
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g1466.t2 | CDD | cd00110 | LamG | 5 | 160 | 5.07306E-22 |
| 5 | g1466.t2 | Gene3D | G3DSA:2.60.120.200 | - | 1 | 186 | 2.3E-48 |
| 12 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 233 | 315 | - |
| 16 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 245 | 263 | - |
| 17 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 266 | 290 | - |
| 18 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 291 | 307 | - |
| 19 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 399 | 422 | - |
| 15 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 460 | 489 | - |
| 14 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 553 | 591 | - |
| 13 | g1466.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 630 | 651 | - |
| 2 | g1466.t2 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 19 | 377 | 5.7E-58 |
| 3 | g1466.t2 | PANTHER | PTHR15036:SF68 | NEUREXIN 1, ISOFORM F | 19 | 377 | 5.7E-58 |
| 1 | g1466.t2 | Pfam | PF02210 | Laminin G domain | 36 | 160 | 1.8E-19 |
| 7 | g1466.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 496 | - |
| 8 | g1466.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 497 | 520 | - |
| 6 | g1466.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 521 | 651 | - |
| 20 | g1466.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 1 | 205 | 24.825 |
| 11 | g1466.t2 | SMART | SM00282 | LamG_3 | 28 | 162 | 3.6E-21 |
| 4 | g1466.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 4 | 160 | 5.54E-27 |
| 10 | g1466.t2 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 498 | 520 | - |
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