General information for g7652.t1
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.t1 | TTS | g7652.t1 | 25081146 | 25081146 |
| chr_2 | g7652 | g7652.t1 | isoform | g7652.t1 | 25081869 | 25087991 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon1 | 25081869 | 25082059 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS1 | 25081869 | 25082059 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon2 | 25082132 | 25082266 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS2 | 25082132 | 25082266 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon3 | 25082331 | 25082869 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS3 | 25082331 | 25082869 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon4 | 25082934 | 25083201 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS4 | 25082934 | 25083201 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon5 | 25083268 | 25083411 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS5 | 25083268 | 25083411 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon6 | 25083473 | 25083682 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS6 | 25083473 | 25083682 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon7 | 25083744 | 25084040 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS7 | 25083744 | 25084040 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon8 | 25084103 | 25084432 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS8 | 25084103 | 25084432 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon9 | 25084491 | 25085862 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS9 | 25084491 | 25085862 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon10 | 25086632 | 25086828 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS10 | 25086632 | 25086828 |
| chr_2 | g7652 | g7652.t1 | exon | g7652.t1.exon11 | 25087985 | 25087991 |
| chr_2 | g7652 | g7652.t1 | cds | g7652.t1.CDS11 | 25087985 | 25087991 |
| chr_2 | g7652 | g7652.t1 | TSS | g7652.t1 | NA | NA |
Sequences
>g7652.t1 Gene=g7652 Length=3690
ATGACTGGTGGCAACGCATGGACATCAGCAGTTTCAGACTTTCAACAATATTTAATCATT
GATTTAGGATCAACGAAAAATATCACTAGAATCTCTATTCAGGGTCGTCCGCATCATAGT
GAATATGTTTCAGAGTTCAGTATAAGCTATGGATACAATGGACTTGATTATGCAGATTTT
AAAGAATCCGGTGGTAATACAAAGCTTTTCAAAGGCAATGAAGATGGTGACAATGTAAAA
CACAACCTATTTGATGTTCCCATCATTGCACAATGGATTCGAGTTAATCCTACTCGATGG
AAAGACCGAATTTCTCTAAGAGTCGAATTATATGGGTGTGATTACGATGCTGAGACTGTT
TACTTTAATGGAACGAGCTTAATGAGTTTAGATTTGTTACATGATCCGATTTCTGCATCT
AGAGAGACACTTCAATTTCGTTTCAAGACTTCACATGCCAATGGAATTCTTATGTACTCG
AAAGGCACTCAAGGAGATTTCTTTGCTTTACAACTCTATGAAAATCGAATGATACTCAAC
ATTAATCTCGGTGCAAGTTCAATGAGTTCATTCTCAGTCGGTAGTTTACTTGATGACAAT
GTTTGGCATGATGTCGTCATATCACGTAATAGACGAGATATTTTATTTTCTGTTGATCGT
GTTGTTGTCGATGGAAAAATCAAAGGTGATTTTGACAAATTAGATCTCAATCGTATGCTT
TATATTGGAGGTGTGCCTGCAAAAGATGAAGGACTTGTTGTAACACAAAACTTTACTGGT
TGTATTGAGAATTTATATTTGAACACAACGAACTTTATTCGCGAACTAAAACAAGCTTAT
GAAGAAAGACAATACAGTCGATTTGAAAAAATAAATACTTTCTACAATTGTCCTGAGCCA
CCAATTATGCCAGTCACTTTCATCACAAGAACATCTTATGCAAAATTGAAAGGTTACGAG
GGTGTTCGAAGCATGAATGTATCACTTTCATTTAGAACATATGAAGATAAAGGTCTCATT
ATTTATCATCCTTTTTCATCTAAAGGATATGTAAAAGTTTTCCTTGAAGATGGTCGTGTA
AAGACAGAAATTAAAACAGATGATAAAGAGATTCACAGCACAGGTGATCATCGACGCGGA
ATCGTTTTAGACAATTATGACGAACAATTCAATGATGGTAGATGGCATTCATTGATTCTT
ACAATTAAACAAAACAGTCTTGTACTTGAAATTGATCAAAAACCAATGCGAACTGAGAAA
CTTTTCTCTATCATTACTGGTTCATGGTATTACATTGGTGGTTCGCCAACAAAAGAAATT
CACAATATTATAACCAATCGAGATGGTTTTATTGGCTGCATGCGACAAATTTCTGTCGAT
GGCAATTTTAAATTACCTCATGATTGGAAAGAAGATGATTTCTGTTGTAAAAATGAAATT
CTTATGGATGCTTGCCATATGATCGATCGATGTAATCCAAACCCATGTAAACACAATGGT
CAATGCCGTCAAAATTCATATGAATTCTTCTGTGAATGTGGAAATTCTGGTTATTCTGGT
GCTGTTTGTCACACATCATTAAATCCATTATCGTGTCAAGCATACAAAAATGTTCAAGCA
GTTGGTCAAAAAGCAAACATTAAAATCGATGTCGATGGCTCAGGACCTCTTGATCCGTTT
GAAGTTACTTGCGAGTTTCTCACTGATGGGCGAGTTCTTACAGTATTGGGTCATTCATCA
GAACACTCAACTGTCGTTGACAGTTTTCAAGAACCTGGCTCTTATGATCAAACAATTGAA
TATAACGCAAAATTACCACAAATTGAAGCTCTTCTTAATCGTTCACATGAATGTTCACAA
AGATTGTCCTACAATTGTCGAAATTCACGTTTATTCAATTCTCCATCTGATGAACAAAAT
TTCCGACCATTTGGATGGTGGTTGTCAAGACAAAATCAAATGATGGACTATTGGGCAGGT
GCACTTCCAGGGTCTCGTAAATGTCAATGTGGCATTGTTGGTAACTGTATTGATCCTACT
AAATGGTGCAATTGTGATGCAAGTTTGTACGATTGGCAGGAGGATAGTGGAGAAATCAAG
GATAAAGAATATCTTCCAGTTCGAGGTTTGAGATTTGGTGATACAGGAACTGCTTTAGAT
GAGAAACAAGCTAAATATACCCTTGGTCCACTTGTATGTGAAGGTGATGATTTATTCAAT
AATGTTGTAACATTTAGAATCACTGATGCTACCATCAATTTACCTCGATTTGATATGGGA
CATTCTGGTGATATTTATTTGGAATTCAAGACAACACAAGAAAATGCAGTTATTTTCCAT
GCAAAAGGATCAACTGACTACATTAAATTGTCTATCATTGGAGGCAACAAGTTAAAATTT
CAATATCAAGCTGGATCTGGTCCACTATCTGTAGATGTCCAAACATCATATCCATTGAAT
GATAATAACTGGCACTCTGTTAGTGTTGAAAGAAATCGTAAGGAAGCTCGTTTAGTCATT
GATGGTGCAACAAAATCTGAAGTTCGTGAACCTCCAGGGCCTGTTCGTGCACTTTATCTT
ACATCAGAATTAGTAATTGGTGCAACACTAGATTATCAAGATGGTTTCGTAGGATGTATT
CGTGCTTTACTGCTAAATGGTTTGCCTGTTGACTTGAAATCGTATGCTGAGAGAAAACTT
TATGGCGTTTCGCCTGGTTGTGTAGGACGATGTGAGAGCAATCCTTGCTTGAATAATGGA
ACATGTTTTGAAAGATATGATGGTTTCTCATGTGATTGTCGTTGGAGTTCATTTAAAGGA
CCAATTTGCGCTGATGAAATTGGTGTAAATTTGCGTTCCGATTCCATCATTAAATACGAT
TTCTTGGGATCATGGCGTTCAACAATTGCTGAAAATATTCGAGTAGGATTTACAACGACA
AATCAAAAAGGATTTTTACTCGGCTTTAGCTCAAATATTACAGGCGAATATTTGACAATT
CTCGTTTCAAATTCTGGTGCCTTGAAATTTGTGTTTGATTTTGGTTTTGAAAGACAAGAA
ATTTCTTTCCCTGGAGTTCATTTTGGTCTCGGTCAATATCATGATGTTCGTTTTACAAGA
AAAAATTCTGGATCAACTGTTGTCATTACTGTGGATAATTACGAGCCAAAAGAATATCAC
TTTGATATTAAAGACTCTGCAGATGCACAATTCAATAATGTTCAATATATGTATATTGGA
AAGAATGAAAGTATGACAGACGGGTTCGTCGGATGTGTATCAAGAGTTGAATTTGACGAC
ATTTTCCCACTTAAATTGCTATTTCAACAGAATCCACCACCAAATGTTAAATCATTAGGT
CCATCTTTATTGACTGAAGATTTTTGCGGTGTCGAACCTGTCACATTACCACCAGTTGAA
AAAGAAACCAGACCACCACCAATTGTTGATGAAGAAAAATTAAGAAGTTATGATGGTTTC
ACTGCAGGATTTCTAGGAAGTCTATTGTTCATTATTCTTTTATTGCTACTTATAATGGCA
ATATTAATTTATCGTCATATGTCACGACATAAGGGAGAATATTTAACACAAGAAGATAAG
GGAGCAGATGATGCTTTAGATCCAGATGATGCTGTTGTTCACTCAACAACTGGTCACCAT
GTCACCAAAAAGAAAGAGTGGTTCATTTAA
>g7652.t1 Gene=g7652 Length=1229
MTGGNAWTSAVSDFQQYLIIDLGSTKNITRISIQGRPHHSEYVSEFSISYGYNGLDYADF
KESGGNTKLFKGNEDGDNVKHNLFDVPIIAQWIRVNPTRWKDRISLRVELYGCDYDAETV
YFNGTSLMSLDLLHDPISASRETLQFRFKTSHANGILMYSKGTQGDFFALQLYENRMILN
INLGASSMSSFSVGSLLDDNVWHDVVISRNRRDILFSVDRVVVDGKIKGDFDKLDLNRML
YIGGVPAKDEGLVVTQNFTGCIENLYLNTTNFIRELKQAYEERQYSRFEKINTFYNCPEP
PIMPVTFITRTSYAKLKGYEGVRSMNVSLSFRTYEDKGLIIYHPFSSKGYVKVFLEDGRV
KTEIKTDDKEIHSTGDHRRGIVLDNYDEQFNDGRWHSLILTIKQNSLVLEIDQKPMRTEK
LFSIITGSWYYIGGSPTKEIHNIITNRDGFIGCMRQISVDGNFKLPHDWKEDDFCCKNEI
LMDACHMIDRCNPNPCKHNGQCRQNSYEFFCECGNSGYSGAVCHTSLNPLSCQAYKNVQA
VGQKANIKIDVDGSGPLDPFEVTCEFLTDGRVLTVLGHSSEHSTVVDSFQEPGSYDQTIE
YNAKLPQIEALLNRSHECSQRLSYNCRNSRLFNSPSDEQNFRPFGWWLSRQNQMMDYWAG
ALPGSRKCQCGIVGNCIDPTKWCNCDASLYDWQEDSGEIKDKEYLPVRGLRFGDTGTALD
EKQAKYTLGPLVCEGDDLFNNVVTFRITDATINLPRFDMGHSGDIYLEFKTTQENAVIFH
AKGSTDYIKLSIIGGNKLKFQYQAGSGPLSVDVQTSYPLNDNNWHSVSVERNRKEARLVI
DGATKSEVREPPGPVRALYLTSELVIGATLDYQDGFVGCIRALLLNGLPVDLKSYAERKL
YGVSPGCVGRCESNPCLNNGTCFERYDGFSCDCRWSSFKGPICADEIGVNLRSDSIIKYD
FLGSWRSTIAENIRVGFTTTNQKGFLLGFSSNITGEYLTILVSNSGALKFVFDFGFERQE
ISFPGVHFGLGQYHDVRFTRKNSGSTVVITVDNYEPKEYHFDIKDSADAQFNNVQYMYIG
KNESMTDGFVGCVSRVEFDDIFPLKLLFQQNPPPNVKSLGPSLLTEDFCGVEPVTLPPVE
KETRPPPIVDEEKLRSYDGFTAGFLGSLLFIILLLLLIMAILIYRHMSRHKGEYLTQEDK
GADDALDPDDAVVHSTTGHHVTKKKEWFI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 25 | g7652.t1 | CDD | cd00057 | FA58C | 1 | 112 | 1.73055E-33 |
| 28 | g7652.t1 | CDD | cd00110 | LamG | 119 | 268 | 8.44544E-31 |
| 31 | g7652.t1 | CDD | cd00110 | LamG | 304 | 460 | 2.35062E-23 |
| 27 | g7652.t1 | CDD | cd00054 | EGF_CA | 488 | 523 | 3.50459E-4 |
| 30 | g7652.t1 | CDD | cd00110 | LamG | 742 | 886 | 1.71996E-27 |
| 26 | g7652.t1 | CDD | cd00054 | EGF_CA | 911 | 943 | 1.40637E-5 |
| 29 | g7652.t1 | CDD | cd00110 | LamG | 948 | 1099 | 2.25478E-16 |
| 21 | g7652.t1 | Gene3D | G3DSA:2.60.120.260 | - | 1 | 116 | 7.0E-35 |
| 17 | g7652.t1 | Gene3D | G3DSA:2.60.120.200 | - | 117 | 287 | 1.4E-40 |
| 20 | g7652.t1 | Gene3D | G3DSA:2.60.120.200 | - | 302 | 473 | 5.2E-27 |
| 16 | g7652.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 487 | 526 | 4.2E-8 |
| 19 | g7652.t1 | Gene3D | G3DSA:2.60.120.200 | - | 740 | 906 | 4.1E-36 |
| 15 | g7652.t1 | Gene3D | G3DSA:2.10.25.10 | Laminin | 907 | 946 | 2.9E-11 |
| 18 | g7652.t1 | Gene3D | G3DSA:2.60.120.200 | - | 950 | 1121 | 1.6E-26 |
| 8 | g7652.t1 | PANTHER | PTHR15036 | PIKACHURIN-LIKE PROTEIN | 4 | 1099 | 1.9E-276 |
| 9 | g7652.t1 | PANTHER | PTHR15036:SF49 | NEUREXIN-4 | 4 | 1099 | 1.9E-276 |
| 3 | g7652.t1 | Pfam | PF00754 | F5/8 type C domain | 4 | 110 | 9.9E-21 |
| 4 | g7652.t1 | Pfam | PF02210 | Laminin G domain | 148 | 269 | 7.2E-25 |
| 5 | g7652.t1 | Pfam | PF02210 | Laminin G domain | 331 | 462 | 1.1E-17 |
| 1 | g7652.t1 | Pfam | PF00008 | EGF-like domain | 491 | 521 | 1.2E-4 |
| 7 | g7652.t1 | Pfam | PF02210 | Laminin G domain | 769 | 887 | 3.8E-24 |
| 2 | g7652.t1 | Pfam | PF00008 | EGF-like domain | 911 | 934 | 1.8E-5 |
| 6 | g7652.t1 | Pfam | PF02210 | Laminin G domain | 977 | 1100 | 7.3E-15 |
| 23 | g7652.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 1161 | - |
| 24 | g7652.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1162 | 1184 | - |
| 22 | g7652.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1185 | 1229 | - |
| 34 | g7652.t1 | ProSitePatterns | PS01285 | Coagulation factors 5/8 type C domain (FA58C) signature 1. | 6 | 35 | - |
| 33 | g7652.t1 | ProSitePatterns | PS01286 | Coagulation factors 5/8 type C domain (FA58C) signature 2. | 97 | 113 | - |
| 42 | g7652.t1 | ProSiteProfiles | PS50022 | Coagulation factors 5/8 type C domain (FA58C) profile. | 1 | 113 | 33.843 |
| 43 | g7652.t1 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 117 | 297 | 39.366 |
| 45 | g7652.t1 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 303 | 485 | 28.796 |
| 48 | g7652.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 487 | 524 | 17.168 |
| 46 | g7652.t1 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 741 | 907 | 36.683 |
| 47 | g7652.t1 | ProSiteProfiles | PS50026 | EGF-like domain profile. | 908 | 944 | 13.95 |
| 44 | g7652.t1 | ProSiteProfiles | PS50025 | Laminin G domain profile. | 946 | 1129 | 23.785 |
| 35 | g7652.t1 | SMART | SM00231 | disc_4 | 1 | 113 | 9.0E-7 |
| 38 | g7652.t1 | SMART | SM00282 | LamG_3 | 140 | 270 | 5.9E-34 |
| 37 | g7652.t1 | SMART | SM00282 | LamG_3 | 323 | 462 | 2.4E-25 |
| 41 | g7652.t1 | SMART | SM00181 | egf_5 | 490 | 524 | 3.7 |
| 39 | g7652.t1 | SMART | SM00282 | LamG_3 | 761 | 888 | 1.8E-33 |
| 40 | g7652.t1 | SMART | SM00181 | egf_5 | 910 | 944 | 0.71 |
| 36 | g7652.t1 | SMART | SM00282 | LamG_3 | 969 | 1101 | 1.9E-16 |
| 10 | g7652.t1 | SUPERFAMILY | SSF49785 | Galactose-binding domain-like | 3 | 116 | 3.06E-32 |
| 11 | g7652.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 107 | 270 | 6.15E-35 |
| 14 | g7652.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 297 | 490 | 3.17E-26 |
| 13 | g7652.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 510 | 907 | 4.19E-32 |
| 12 | g7652.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 915 | 1099 | 1.17E-22 |
| 32 | g7652.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 1162 | 1184 | - |
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 K07380 (contactin associated protein-like 2)
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.
