General information for g9435.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neuroligin-1.
Parent gene
- The parent gene g9435 is located on chr_1: 2972707..3035514 (- 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_1 | g9435 | g9435.t1 | isoform | g9435.t1 | 2972707 | 3035514 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon1 | 2972707 | 2973374 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS1 | 2972707 | 2973374 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon2 | 2976955 | 2977049 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS2 | 2976955 | 2977049 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon3 | 2977108 | 2977259 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS3 | 2977108 | 2977259 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon4 | 2981088 | 2981226 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS4 | 2981088 | 2981226 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon5 | 2981284 | 2981496 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS5 | 2981284 | 2981496 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon6 | 2981575 | 2981719 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS6 | 2981575 | 2981719 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon7 | 2981860 | 2982150 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS7 | 2981860 | 2982150 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon8 | 2982831 | 2982980 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS8 | 2982831 | 2982980 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon9 | 2983046 | 2983225 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS9 | 2983046 | 2983225 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon10 | 3013876 | 3014039 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS10 | 3013876 | 3014039 |
| chr_1 | g9435 | g9435.t1 | exon | g9435.t1.exon11 | 3035234 | 3035514 |
| chr_1 | g9435 | g9435.t1 | cds | g9435.t1.CDS11 | 3035234 | 3035514 |
| chr_1 | g9435 | g9435.t1 | TSS | g9435.t1 | NA | NA |
| chr_1 | g9435 | g9435.t1 | TTS | g9435.t1 | NA | NA |
Sequences
>g9435.t1 Gene=g9435 Length=2478
ATGTTGCTCATAGCTTTGCTCATAACTCTATTGACACCGACAATATCATCGGGTGGTGAT
GATTCATCATCAAATGATCAATCACAAATACCATCAAGAATTGTGCATACAAAATATGGA
GCAGTTTCAGGCACAATTGTGCAATTAGAAAGTTTAAATCGCAATCTCGGTCCTGTCGAG
GTGTTCAAAGGTATTCCATATGCTTCACCGCCCATTGGATCATTGAGATTTATGCCGCCA
GTCACTGGAGCATTATGGCCGGGTGTCAAAAAGGCTGACAGATTTAGCGCAGTTTGTCCA
CAACGATTGCCAGACATATCAAATGAAACAGAGGCATTAGAAAGAATGCCAAAAGGCAGA
TATGAATATTTAAAGCGATTGCTGCCATATCTACAAAATCAATCAGAAGATTGTCTTTAT
CTTAACATTTATGCGCCCATTCAAGCTGGCTCGAGAGGCGACAGCAGCGGTAATGGAAAT
GCGAATCCTGTGAAATATCCTGTGATGGTGTTTGTTCATGGTGAATCGTATGAATGGAAT
AGCGGCAATGCTTACGATGGTAGTGCATTAGCTAGTTATGGCCAAATTTTAGTCGTTACA
ATCAATTATCGATTAGGCATTCTTGGTTTCCTAAATGCAAATGTCGATCGTTATTCAAAG
TCACCTGCCAATTACGGTCTAATGGATATTTTAGCAGCATTGCATTGGATACAGGAAAAT
ATTGAGGCATTTGGCGGTGACAATAAGAGCGTGACATTAGCTGGACATGGATCAGGTGCA
GCTTGTGTTCATTTTCTAATTGCCTCACAGGCCGTGCCTGATAGCCTTTTATTTCATCGT
GCAATATTAATGTCAGGCACAGGTCTTGCACCATGGTCACTTGTTGGTGATCCTGCCTAT
TATGCTGCCATTGTTGCGCATCATGTTAATTGTTCTGTTGACTTACCTCATCAAGCTTTA
ATGAAATGTCTTCGTGATGTTTCACTCAAGTCACTACTTTCAACACCTGTACGTGTGCCC
GATTTCGGCAATGCATTTGGACCAAGTGTCGATGGTGTTGTTATTGATACGGGTGATTTT
AGTCAGCAGGATCCATATGATTTTGGATCACTCAGTGGTAGTGATACAAAACGACAAATG
CACTATCAAAATAATCTCAATATAATAAATTCAGTATTGTTAAGGAAATTAGCTATAAAC
AAATTATCAAGATACGATTTATTGGTAGGCGTTACACGTGCTGAGTCATATTTTATTTTT
AATGCTGGTGACGTTCAGTATGGCATTGAGTCAGATAGAAAGACAAAAATTTTAAGAAAT
TATGTAAGAAGTACTTATAGCTATCATTTGAATGAAATTCTCGCAACAATTGAGAATGAA
TATAAAGACTGGGAAAAACCTGTTCAACATCCAATAAATATACGTGATGAAACATTAGAA
GCATTAAGTGATGCTCAAGTTGTTGCTCCGGCCACTTTAACTGTTGATTTACATTCTGCT
GATCATCGAAATTCATTTCTTTATGTGTTCGATTATCAAACTAAATTTGGAGATTATCCT
CAGCGACAGGGATGCATACATGGCGAGGATTTACCATACTTTTTTGGAGCACCACTCGTC
GGTGGACTCAGTCATTTTGCTAAAAATTTTACAAAAGCAGAAATTTTGCTGTCTGAAATT
GTGATGAATTATTGGTCCAATTTTGTAAGAACAGGTAATCCAAATGAACAACAAGATAAT
CGAGATAGAAAAGCAAAAAATATTGAATGGACGCCATATGAGAATGTTCATAAAAAGTAC
CTTAATATTGATACAAAACCAAAACTAAAAAATCATTATCGTGCTCATCGTCTATCATTT
TGGCTCAATTTAATTCCTGACCTTCATAAGCCAGGGAATGATGATGTGCCATTATCGCAC
CATGAATTGGAAAATGATGATGTTGTTGATCAAAGCAAATCGACAGTTAAACCATTGATA
CCACAACGTGATAAAGGAGCAAATGGAACATCACCTAATAGTACAGTACTTTTCTCATCG
CCAATTTTTAATTATACATTGCAGCGCAGTAACAATCGCAATAATAGTGGATCACATAAT
GCTCAAATAAATTCAAATTTGTCAGGCGGCAAAACGAAAAGCAATGTGCCTGGCATCGAC
CATGATATGTACGATGAGAATGCAACATCGGGACCACCAACAGAAGATGGTTTTGCTGCA
TATAGCACAGCATTAAGCGTAACAATTGCAATTGGCTGCAGTCTATTAATTCTCAATGTG
CTCATTTTTGCTGGCGTTTATTATCAACGTGACAAGACTCGACTCAATGAGCCGAGAACG
ATAAAAAAGCGTAATGAAAATGGTCAAATGCCAAACAATATTTGTGGTGATCTTGAAACA
CTTACAATTCATTCAAAAAGTGATCCTGCCACGATTCTTGGTCATCATCATTCATTGCAT
CAACTGCCACCACCTTGA
>g9435.t1 Gene=g9435 Length=825
MLLIALLITLLTPTISSGGDDSSSNDQSQIPSRIVHTKYGAVSGTIVQLESLNRNLGPVE
VFKGIPYASPPIGSLRFMPPVTGALWPGVKKADRFSAVCPQRLPDISNETEALERMPKGR
YEYLKRLLPYLQNQSEDCLYLNIYAPIQAGSRGDSSGNGNANPVKYPVMVFVHGESYEWN
SGNAYDGSALASYGQILVVTINYRLGILGFLNANVDRYSKSPANYGLMDILAALHWIQEN
IEAFGGDNKSVTLAGHGSGAACVHFLIASQAVPDSLLFHRAILMSGTGLAPWSLVGDPAY
YAAIVAHHVNCSVDLPHQALMKCLRDVSLKSLLSTPVRVPDFGNAFGPSVDGVVIDTGDF
SQQDPYDFGSLSGSDTKRQMHYQNNLNIINSVLLRKLAINKLSRYDLLVGVTRAESYFIF
NAGDVQYGIESDRKTKILRNYVRSTYSYHLNEILATIENEYKDWEKPVQHPINIRDETLE
ALSDAQVVAPATLTVDLHSADHRNSFLYVFDYQTKFGDYPQRQGCIHGEDLPYFFGAPLV
GGLSHFAKNFTKAEILLSEIVMNYWSNFVRTGNPNEQQDNRDRKAKNIEWTPYENVHKKY
LNIDTKPKLKNHYRAHRLSFWLNLIPDLHKPGNDDVPLSHHELENDDVVDQSKSTVKPLI
PQRDKGANGTSPNSTVLFSSPIFNYTLQRSNNRNNSGSHNAQINSNLSGGKTKSNVPGID
HDMYDENATSGPPTEDGFAAYSTALSVTIAIGCSLLILNVLIFAGVYYQRDKTRLNEPRT
IKKRNENGQMPNNICGDLETLTIHSKSDPATILGHHHSLHQLPPP
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9435.t1 | Gene3D | G3DSA:3.40.50.1820 | - | 25 | 638 | 1.7E-172 |
| 2 | g9435.t1 | PANTHER | PTHR43903:SF21 | NEUROLIGIN 3, ISOFORM B | 12 | 825 | 0.0 |
| 3 | g9435.t1 | PANTHER | PTHR43903 | NEUROLIGIN | 12 | 825 | 0.0 |
| 1 | g9435.t1 | Pfam | PF00135 | Carboxylesterase family | 32 | 621 | 4.1E-137 |
| 10 | g9435.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 11 | g9435.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 12 | g9435.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 12 | - |
| 14 | g9435.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 18 | - |
| 9 | g9435.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 737 | - |
| 13 | g9435.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 738 | 768 | - |
| 8 | g9435.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 769 | 825 | - |
| 17 | g9435.t1 | ProSitePatterns | PS00941 | Carboxylesterases type-B signature 2. | 136 | 146 | - |
| 4 | g9435.t1 | SUPERFAMILY | SSF53474 | alpha/beta-Hydrolases | 33 | 629 | 3.21E-114 |
| 6 | g9435.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 15 | g9435.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 5 | g9435.t1 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
| 16 | g9435.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 744 | 766 | - |
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 K07378 (neuroligin)
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