General information for g1468.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neurexin-3.
Parent gene
- The parent gene g1468 is located on chr_3: 11090244..11142072 (- 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 | g1468 | g1468.t2 | isoform | g1468.t2 | 11090244 | 11142072 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon1 | 11090244 | 11090323 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS1 | 11090244 | 11090323 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon2 | 11091984 | 11092741 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS2 | 11091984 | 11092741 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon3 | 11094349 | 11094496 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS3 | 11094349 | 11094496 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon4 | 11114337 | 11114448 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS4 | 11114337 | 11114448 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon5 | 11115961 | 11116722 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS5 | 11115961 | 11116722 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon6 | 11117053 | 11117472 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS6 | 11117053 | 11117472 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon7 | 11117589 | 11117776 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS7 | 11117589 | 11117776 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon8 | 11118970 | 11119119 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS8 | 11118970 | 11119119 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon9 | 11120893 | 11121028 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS9 | 11120893 | 11121028 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon10 | 11127108 | 11127164 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS10 | 11127108 | 11127164 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon11 | 11127229 | 11127507 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS11 | 11127229 | 11127507 |
| chr_3 | g1468 | g1468.t2 | exon | g1468.t2.exon12 | 11141491 | 11142072 |
| chr_3 | g1468 | g1468.t2 | cds | g1468.t2.CDS12 | 11141491 | 11142072 |
| chr_3 | g1468 | g1468.t2 | TSS | g1468.t2 | NA | NA |
| chr_3 | g1468 | g1468.t2 | TTS | g1468.t2 | NA | NA |
Sequences
>g1468.t2 Gene=g1468 Length=3672
ATGGCGGAATATGATAATTTACAATTACAATCCAATTATCAAACCAATCATAAACATAAA
CATAACAATAATGTAAGCAGCATAGGAAGACGCAGTGATGACAATGTAAAAATGATGGCG
CTAAAGTGTCAAAGGCCAACAACAATCATGAGCCATCATCAGTTAGTTAATAAGTGCTAT
ACAACTATTTGCAACGATAATAATCACAATAAATTCTATAGATTGCCCATCAGAAAATTC
AACTTTAGTTGTTATAATAAATCATTTATGCTAGCGTTGTTATTAGTGCTCGGTTTATTT
TTTGAAATGACATCATGCGAGGGATTTCAGTTGGAAGGCACTGAAAATTCTTATGCACAA
TTTCGCAAATGGTATTCGGGATTGAATGGCTCACTTGAGCTTGAATTTAAAACGGAACAG
CCAAATGGTTTGGTTTTGTATACGGATGATGGTGGCACTTATGATTTCTTCGAATTGAAG
CTTGTTGAAGGTGCTTTGCGACTACGTTACAATCTTGGTGGTGGAGCACAAATAATTACT
GTTGGTAGAGATCTTCATGATGGACATTGGCATAAAGTTCAGGTGCTTCGTAATGATGAA
CATACAACACTAACAGTCGATGGAGTGTCACAAAGTAAAGCATCACGTGGTAAAGAATTT
CAATTTGGAAAATTTGCAACAAATTCGGATATTTTTGTTGGTGGCATGCCGACTTGGTAT
AATGCAAAATTAGCCATGCTAGCACTGCCGAGTGTCATTTTTGAGCCAAGATTTCGTGGA
TCAGTGAGAAATTTAGTTTATACAGATCAGCCTGGTGTTTTACCAAGACGTCAAGAAATG
CGACAACCGAGAGATGCAAAGTGTGGAGATTCTGTGTGCGATCAAGCTGATATGATGCCA
GAGAAGAAAGTCACTCGTGGTTTACGTAACAACGTCACAGATGCTTGTGAACGACACGAC
CCATGTCAACATGGCGGCATTTGTATTTCAACTGATTCAGGTCCATTATGTGAATGCCGT
AATTTGGAGTACGAGGGCACTTATTGTGAACGAGACAAAGCACCAAGCGAAGCAACATTC
CGGGGCACTGAATTTCTATCATATGATTTGGGACAGACAGGCGGAGAACCGATTGTTAGT
GCACAAGATGCAATTTCATTATATTTTCGAACTAGACAGCCTAATGGATTGTTATTCTTT
ACTGGTCATGGAACTGACTATTTGAATCTGGCAATTCGTGATGGTGGAGTTTCATTAACA
ATGGGTTTGGCAAATGGTAAACAGGAAATGCACATAAAGCCTGCTCGCGTGCGCTTCGAT
GATCATCAATGGCACAAAGTGACAGTACATCGTAGAATTCAGGAAATTTCATCAATTACG
AGTTTCTGTCGGCTTGTTGTGGTTGTCGATGAGGTTTATACGGATCATTCACACATTGCC
GGTAAATTCACAATACTCTCATCATCAAAGGTCTATGTGGGTGGCTCGGTAAATCCAAGA
GCATTGCTTGGTGCTCGTGTGCATAACAACTTTGTTGGTTGTTTGAGAAAAGTTGAATTT
TCTGCAGACACGCTTCGATTAAATTTAATTGATTTAGCAAGAACTGGTTCAAAATTGATT
CAAGTTGTTGGCAGAGTTGAATATAATTGTCCATCAGGTGACCCACAAGATCCTGTCACT
TTCACCACACGTGATTCACATTTAGTTTTGCCACCATGGGAAGTATCTAAACAAGGTGTT
ATAAGTTTCAAATTTCGCACAAATGAACCTAATGGAATGATTATTTTGGCAACTGGAACT
AAACCACCTAGGTCTGATTTCTTTGCTGTCGAGTTGCTTAATGGACACATTTATGTTCAT
ATTGATCTCGGTTCGGGTGCTTCGAAAGTGCGAGCATCAAGACGACGAGTTGATGATGGT
GTCTGGCACGAATTGATTTTAAGGAGAAGTGGCCGCGAGGGAAAAGTTGGAGTTGATGGA
CAATATAATGACTTTAAAACACCAGGTGATTCAACACAGCTTGAGCTCGATAGTCCGCTT
TATATTGGTGGTATTGGACCGAGTTATGCAAATGTAAATGTTCCACCAGCATTATGGACT
GGTACACTACGTCAAGGTTATGTTGGATGCCTAAGAGATTTGGTATTAAGTGGTAAACCA
GTAGATATTGCTGCTTATGCAAGACAACAAGACACAGCAGCTGTAAAACCATCTTGTCAC
GTTCAAACCGTTCAATGTACACCAAATCCTTGCCATAATGGTGGTGTATGCTCTGAGGGA
TGGAATCGACCGTTATGTGACTGCTCAGCAACTTTATATACTGGACCGACATGTGGACGT
GAATCAGCGACTTTAGCATTCAATGGATCACAACATTTGACAATTTGGACGAATGGTTTT
GCAAATCAAGGTGTAAGAACTCAAACGGAAGAACTTGTGTTAAGATTTAAAACATCAAGA
CCTACTGGATTGCTATTATTGACTAGTGCAGATACAAATTCACCAGATCGACTTGAAATT
GCTCTCGTTGCAGGAAGAGTTAGAGCAAATGTTCGTTTGGGTGATCGTGAAAAGAACTTG
TTGGCTGGTCAGGGTGTTCTAAATGACAATAATTGGCATACGGTGAGATTTTCACGTAGA
GCATCCAATTTGCGTCTTCAGGTTGACGGGGCTATCCCCGTGCGTGCTGAAACAATTTTG
GGACGTCATAGTACTTTGGAAGTAAGATCATTGCATTTGGGTGGACTTTTCCATGCAGAA
GAAGAAATTCAAATGACAGCAACAATGCCAAACTTTGTTGGACAATTGCAAGGTTTTGTT
TACAATGGGCATAGATACATTGATGTAGTGAAATCATTGGGTCCAGAATTAAATGCAATT
CCACAAACCACTTTCAAGTTGACAGCACGTTTTGTGAATGTTCCACCAGGCAGTCCTTAT
AAAGTGGCCACATTCAAGTCAAAGCACTCATATGTCGGTCTAGCCATGCTCAAGGCATTC
GATTCTGTCTCTATTGACTTCCGTTTCAAAACTCTTGAACCAAATGGCATTCTATTTTTC
AATGGCGGCAAAAAGAATGACTTTATATGTATAGAACTGGTCAACGGTCACATTCATTAT
ATTTTCGACATGGGTGATGGCATGGTGACGATGCGTGACAAGAGCAAAGTTCATATGAAT
GATAACCGTTGGCATTCAGTTAGCATAAGACGACCCGGACCCAAAACACATTCACTTATT
GTCGATGACTCGCTGGAGACAATGGTGACTAGTAGCAATTCAATGCATTTAAAATTGGAT
GGAATTTTATATATTGGTGGTGTTTTTAAAGACATGTATGCAGTTCTGCCTGTAGGAATC
GCTACAAGGTCTGGCTTTGAAGGTTGCTTGGCTTCACTTGATTTGGGTGATTTGTCACCA
AGTCTAATTGATGATGCTGTTGTGCAAAGCACATTAGTAATCAATGGATGTGAAGGACCA
ACAAAATGTAGCCAAAATGCATGCGCCAATCATGGAACTTGTGTTCAACAATGGAATGCT
TATGCTTGTGAATGTGATATGACATCGTATACAGGACCAACTTGTTATGATGAATCAGTG
TCATATGAATTTGGTGCTGTCGTTGGTCTTATACAATTATCAATTTCCACCTGGAAATCA
GCCAGACACTGA
>g1468.t2 Gene=g1468 Length=1223
MAEYDNLQLQSNYQTNHKHKHNNNVSSIGRRSDDNVKMMALKCQRPTTIMSHHQLVNKCY
TTICNDNNHNKFYRLPIRKFNFSCYNKSFMLALLLVLGLFFEMTSCEGFQLEGTENSYAQ
FRKWYSGLNGSLELEFKTEQPNGLVLYTDDGGTYDFFELKLVEGALRLRYNLGGGAQIIT
VGRDLHDGHWHKVQVLRNDEHTTLTVDGVSQSKASRGKEFQFGKFATNSDIFVGGMPTWY
NAKLAMLALPSVIFEPRFRGSVRNLVYTDQPGVLPRRQEMRQPRDAKCGDSVCDQADMMP
EKKVTRGLRNNVTDACERHDPCQHGGICISTDSGPLCECRNLEYEGTYCERDKAPSEATF
RGTEFLSYDLGQTGGEPIVSAQDAISLYFRTRQPNGLLFFTGHGTDYLNLAIRDGGVSLT
MGLANGKQEMHIKPARVRFDDHQWHKVTVHRRIQEISSITSFCRLVVVVDEVYTDHSHIA
GKFTILSSSKVYVGGSVNPRALLGARVHNNFVGCLRKVEFSADTLRLNLIDLARTGSKLI
QVVGRVEYNCPSGDPQDPVTFTTRDSHLVLPPWEVSKQGVISFKFRTNEPNGMIILATGT
KPPRSDFFAVELLNGHIYVHIDLGSGASKVRASRRRVDDGVWHELILRRSGREGKVGVDG
QYNDFKTPGDSTQLELDSPLYIGGIGPSYANVNVPPALWTGTLRQGYVGCLRDLVLSGKP
VDIAAYARQQDTAAVKPSCHVQTVQCTPNPCHNGGVCSEGWNRPLCDCSATLYTGPTCGR
ESATLAFNGSQHLTIWTNGFANQGVRTQTEELVLRFKTSRPTGLLLLTSADTNSPDRLEI
ALVAGRVRANVRLGDREKNLLAGQGVLNDNNWHTVRFSRRASNLRLQVDGAIPVRAETIL
GRHSTLEVRSLHLGGLFHAEEEIQMTATMPNFVGQLQGFVYNGHRYIDVVKSLGPELNAI
PQTTFKLTARFVNVPPGSPYKVATFKSKHSYVGLAMLKAFDSVSIDFRFKTLEPNGILFF
NGGKKNDFICIELVNGHIHYIFDMGDGMVTMRDKSKVHMNDNRWHSVSIRRPGPKTHSLI
VDDSLETMVTSSNSMHLKLDGILYIGGVFKDMYAVLPVGIATRSGFEGCLASLDLGDLSP
SLIDDAVVQSTLVINGCEGPTKCSQNACANHGTCVQQWNAYACECDMTSYTGPTCYDESV
SYEFGAVVGLIQLSISTWKSARH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 36 | g1468.t2 | CDD | cd00110 | LamG | 114 | 267 | 7.47946E-31 |
| 33 | g1468.t2 | CDD | cd00054 | EGF_CA | 314 | 350 | 3.96852E-7 |
| 37 | g1468.t2 | CDD | cd00110 | LamG | 358 | 520 | 2.04157E-24 |
| 39 | g1468.t2 | CDD | cd00110 | LamG | 558 | 716 | 3.34222E-32 |
| 32 | g1468.t2 | CDD | cd00054 | EGF_CA | 747 | 778 | 2.42298E-4 |
| 38 | g1468.t2 | CDD | cd00110 | LamG | 784 | 942 | 5.11786E-22 |
| 35 | g1468.t2 | CDD | cd00110 | LamG | 987 | 1135 | 3.86468E-32 |
| 34 | g1468.t2 | CDD | cd00054 | EGF_CA | 1154 | 1195 | 9.33015E-5 |
| 26 | g1468.t2 | Gene3D | G3DSA:2.60.120.200 | - | 111 | 279 | 7.8E-37 |
| 22 | g1468.t2 | Gene3D | G3DSA:2.10.25.10 | Laminin | 280 | 353 | 2.3E-6 |
| 27 | g1468.t2 | Gene3D | G3DSA:2.60.120.200 | - | 354 | 545 | 3.1E-49 |
| 24 | g1468.t2 | Gene3D | G3DSA:2.60.120.200 | - | 556 | 739 | 1.6E-52 |
| 23 | g1468.t2 | Gene3D | G3DSA:2.10.25.10 | Laminin | 742 | 779 | 1.9E-13 |
| 28 | g1468.t2 | Gene3D | G3DSA:2.60.120.200 | - | 780 | 956 | 1.7E-33 |
| 25 | g1468.t2 | Gene3D | G3DSA:2.60.120.200 | - | 980 | 1158 | 5.3E-43 |
| 21 | g1468.t2 | Gene3D | G3DSA:2.10.25.10 | Laminin | 1159 | 1198 | 7.8E-14 |
| 9 | g1468.t2 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 135 | 797 | 0.0 |
| 12 | g1468.t2 | PANTHER | PTHR15036:SF68 | NEUREXIN 1, ISOFORM F | 135 | 797 | 0.0 |
| 11 | g1468.t2 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 808 | 949 | 0.0 |
| 14 | g1468.t2 | PANTHER | PTHR15036:SF68 | NEUREXIN 1, ISOFORM F | 808 | 949 | 0.0 |
| 10 | g1468.t2 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 949 | 1217 | 0.0 |
| 13 | g1468.t2 | PANTHER | PTHR15036:SF68 | NEUREXIN 1, ISOFORM F | 949 | 1217 | 0.0 |
| 8 | g1468.t2 | Pfam | PF02210 | Laminin G domain | 136 | 269 | 1.9E-26 |
| 3 | g1468.t2 | Pfam | PF12661 | Human growth factor-like EGF | 322 | 339 | 0.036 |
| 5 | g1468.t2 | Pfam | PF02210 | Laminin G domain | 389 | 521 | 4.8E-24 |
| 4 | g1468.t2 | Pfam | PF02210 | Laminin G domain | 585 | 719 | 8.0E-27 |
| 2 | g1468.t2 | Pfam | PF00008 | EGF-like domain | 746 | 776 | 9.4E-5 |
| 7 | g1468.t2 | Pfam | PF02210 | Laminin G domain | 816 | 944 | 3.6E-22 |
| 6 | g1468.t2 | Pfam | PF02210 | Laminin G domain | 1009 | 1136 | 5.9E-27 |
| 1 | g1468.t2 | Pfam | PF00008 | EGF-like domain | 1163 | 1193 | 7.1E-5 |
| 29 | g1468.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 83 | - |
| 31 | g1468.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 84 | 101 | - |
| 30 | g1468.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 102 | 1223 | - |
| 50 | g1468.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 108 | 293 | 37.751 |
| 53 | g1468.t2 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 312 | 350 | 16.505 |
| 51 | g1468.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 355 | 550 | 32.657 |
| 49 | g1468.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 557 | 739 | 44.35 |
| 55 | g1468.t2 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 742 | 779 | 15.296 |
| 48 | g1468.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 784 | 964 | 25.209 |
| 52 | g1468.t2 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 981 | 1157 | 40.489 |
| 54 | g1468.t2 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 1159 | 1196 | 14.744 |
| 43 | g1468.t2 | SMART | SM00282 | LamG_3 | 128 | 270 | 5.8E-32 |
| 45 | g1468.t2 | SMART | SM00181 | egf_5 | 315 | 350 | 0.05 |
| 42 | g1468.t2 | SMART | SM00282 | LamG_3 | 381 | 523 | 3.0E-24 |
| 41 | g1468.t2 | SMART | SM00282 | LamG_3 | 577 | 719 | 4.3E-34 |
| 46 | g1468.t2 | SMART | SM00181 | egf_5 | 745 | 779 | 18.0 |
| 40 | g1468.t2 | SMART | SM00282 | LamG_3 | 808 | 944 | 2.1E-26 |
| 44 | g1468.t2 | SMART | SM00282 | LamG_3 | 1001 | 1138 | 7.9E-35 |
| 47 | g1468.t2 | SMART | SM00181 | egf_5 | 1156 | 1196 | 33.0 |
| 19 | g1468.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 106 | 267 | 1.21E-33 |
| 16 | g1468.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 321 | 520 | 2.06E-30 |
| 17 | g1468.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 549 | 739 | 6.9E-37 |
| 18 | g1468.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 750 | 942 | 7.92E-34 |
| 15 | g1468.t2 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 982 | 1161 | 1.03E-33 |
| 20 | g1468.t2 | SUPERFAMILY | SSF57196 | EGF/Laminin | 1162 | 1195 | 1.48E-5 |
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