General information for g7652.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neurexin-4.
Parent gene
- The parent gene g7652 is located on chr_2: 25085235..25092159 (- 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 | g7652 | g7652.t3 | isoform | g7652.t3 | 25085235 | 25092159 |
| chr_2 | g7652 | g7652.t3 | exon | g7652.t3.exon1 | 25085235 | 25085862 |
| chr_2 | g7652 | g7652.t3 | cds | g7652.t3.CDS1 | 25085236 | 25085862 |
| chr_2 | g7652 | g7652.t3 | exon | g7652.t3.exon2 | 25086632 | 25086828 |
| chr_2 | g7652 | g7652.t3 | cds | g7652.t3.CDS2 | 25086632 | 25086828 |
| chr_2 | g7652 | g7652.t3 | exon | g7652.t3.exon3 | 25090195 | 25090308 |
| chr_2 | g7652 | g7652.t3 | cds | g7652.t3.CDS3 | 25090195 | 25090308 |
| chr_2 | g7652 | g7652.t3 | exon | g7652.t3.exon4 | 25091629 | 25092159 |
| chr_2 | g7652 | g7652.t3 | cds | g7652.t3.CDS4 | 25091629 | 25091689 |
| chr_2 | g7652 | g7652.t3 | TSS | g7652.t3 | NA | NA |
| chr_2 | g7652 | g7652.t3 | TTS | g7652.t3 | NA | NA |
Sequences
>g7652.t3 Gene=g7652 Length=1470
TAGTTGCTAAAGTATTATTTTTATAATAATTTATAAATTTTAATATTTCTCAATTGTAAA
TAAACAATGACTCATAATGAATGAAAGAAAAATTTTGCAATGTCTGTCTATTTTCAATGA
AATTCAATACTTTATTTTACTTACAAAAGAATGATTATGTTTAAGCTAAAGCATAACTAA
AACTTTTCATAATTTACGTCTAATGAAGAAATTAATTGATAATAATCAACTAATTTTTTA
CTTATCTGACATAGGCACCTAATTTTTGAATTTTTAATTGCATGAGTTTCGTAGAGATGT
GCAAGAATGCTAGTTTTTCAATATAACGTAACGGTTGAAGAAATTCGAAACATGTGATAG
TAGTTGTGCAAAGAAGAGTATGCGGCAACCCAAAATTAAGCAGAGAGTAGTGAGTGACTG
TTTGAAAAATTCATCCTCTCATTTCATGTTTAACTTTAAAAGGATAAAGGATGAAAAACT
TAATAATTTTACTGCTAATTAGTGTGTTCTCAATTAGTGTTTTAAGTGCAGAAATTGATT
ATGATGATGATGATATTGAATGCAATGTTCCATTATTGGAAGGAGCAGTTTTAACAGCAA
CATCTTCTCTTAACGAACGTGGACCAGAAAATGCTAGATTAAATGGTGGCAACGCATGGA
CATCAGCAGTTTCAGACTTTCAACAATATTTAATCATTGATTTAGGATCAACGAAAAATA
TCACTAGAATCTCTATTCAGGGTCGTCCGCATCATAGTGAATATGTTTCAGAGTTCAGTA
TAAGCTATGGATACAATGGACTTGATTATGCAGATTTTAAAGAATCCGGTGGTAATACAA
AGCTTTTCAAAGGCAATGAAGATGGTGACAATGTAAAACACAACCTATTTGATGTTCCCA
TCATTGCACAATGGATTCGAGTTAATCCTACTCGATGGAAAGACCGAATTTCTCTAAGAG
TCGAATTATATGGGTGTGATTACGATGCTGAGACTGTTTACTTTAATGGAACGAGCTTAA
TGAGTTTAGATTTGTTACATGATCCGATTTCTGCATCTAGAGAGACACTTCAATTTCGTT
TCAAGACTTCACATGCCAATGGAATTCTTATGTACTCGAAAGGCACTCAAGGAGATTTCT
TTGCTTTACAACTCTATGAAAATCGAATGATACTCAACATTAATCTCGGTGCAAGTTCAA
TGAGTTCATTCTCAGTCGGTAGTTTACTTGATGACAATGTTTGGCATGATGTCGTCATAT
CACGTAATAGACGAGATATTTTATTTTCTGTTGATCGTGTTGTTGTCGATGGAAAAATCA
AAGGTGATTTTGACAAATTAGATCTCAATCGTATGCTTTATATTGGAGGTGTGCCTGCAA
AAGATGAAGGACTTGTTGTAACACAAAACTTTACTGGTTGTATTGAGAATTTATATTTGA
ACACAACGAACTTTATTCGCGAACTAAAAC
>g7652.t3 Gene=g7652 Length=333
MKNLIILLLISVFSISVLSAEIDYDDDDIECNVPLLEGAVLTATSSLNERGPENARLNGG
NAWTSAVSDFQQYLIIDLGSTKNITRISIQGRPHHSEYVSEFSISYGYNGLDYADFKESG
GNTKLFKGNEDGDNVKHNLFDVPIIAQWIRVNPTRWKDRISLRVELYGCDYDAETVYFNG
TSLMSLDLLHDPISASRETLQFRFKTSHANGILMYSKGTQGDFFALQLYENRMILNINLG
ASSMSSFSVGSLLDDNVWHDVVISRNRRDILFSVDRVVVDGKIKGDFDKLDLNRMLYIGG
VPAKDEGLVVTQNFTGCIENLYLNTTNFIRELK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g7652.t3 | CDD | cd00057 | FA58C | 41 | 168 | 7.01116E-42 |
| 17 | g7652.t3 | CDD | cd00110 | LamG | 175 | 324 | 4.37029E-31 |
| 10 | g7652.t3 | Gene3D | G3DSA:2.60.120.260 | - | 30 | 172 | 1.6E-40 |
| 9 | g7652.t3 | Gene3D | G3DSA:2.60.120.200 | - | 173 | 332 | 3.9E-41 |
| 3 | g7652.t3 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 54 | 333 | 3.4E-73 |
| 4 | g7652.t3 | PANTHER | PTHR15036:SF49 | NEUREXIN-4 | 54 | 333 | 3.4E-73 |
| 1 | g7652.t3 | Pfam | PF00754 | F5/8 type C domain | 42 | 166 | 2.3E-26 |
| 2 | g7652.t3 | Pfam | PF02210 | Laminin G domain | 204 | 325 | 8.2E-26 |
| 12 | g7652.t3 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 13 | g7652.t3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 14 | g7652.t3 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 15 | - |
| 15 | g7652.t3 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 16 | 19 | - |
| 11 | g7652.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 333 | - |
| 20 | g7652.t3 | ProSitePatterns | PS01285 | Coagulation factors 5/8 type C domain (FA58C) signature 1. | 62 | 91 | - |
| 19 | g7652.t3 | ProSitePatterns | PS01286 | Coagulation factors 5/8 type C domain (FA58C) signature 2. | 153 | 169 | - |
| 23 | g7652.t3 | ProSiteProfiles | PS50022 | Coagulation factors 5/8 type C domain (FA58C) profile. | 31 | 169 | 35.591 |
| 24 | g7652.t3 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 173 | 333 | 37.669 |
| 21 | g7652.t3 | SMART | SM00231 | disc_4 | 30 | 169 | 1.1E-21 |
| 22 | g7652.t3 | SMART | SM00282 | LamG_3 | 196 | 326 | 5.9E-34 |
| 5 | g7652.t3 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 34 | 172 | 1.98E-38 |
| 6 | g7652.t3 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 163 | 326 | 6.34E-36 |
| 8 | g7652.t3 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 18 | g7652.t3 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 7 | g7652.t3 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 19 | - |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
