General information for g12296.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Neuroglian.
Parent gene
- The parent gene g12296 is located on chr_1: 22242124..22243213 (+ 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 | g12296 | g12296.t6 | isoform | g12296.t6 | 22236087 | 22239648 |
| chr_1 | g12296 | g12296.t6 | exon | g12296.t6.exon1 | 22236087 | 22237734 |
| chr_1 | g12296 | g12296.t6 | cds | g12296.t6.CDS1 | 22237326 | 22237734 |
| chr_1 | g12296 | g12296.t6 | exon | g12296.t6.exon2 | 22238387 | 22238960 |
| chr_1 | g12296 | g12296.t6 | cds | g12296.t6.CDS2 | 22238387 | 22238960 |
| chr_1 | g12296 | g12296.t6 | exon | g12296.t6.exon3 | 22239022 | 22239368 |
| chr_1 | g12296 | g12296.t6 | cds | g12296.t6.CDS3 | 22239022 | 22239368 |
| chr_1 | g12296 | g12296.t6 | exon | g12296.t6.exon4 | 22239432 | 22239648 |
| chr_1 | g12296 | g12296.t6 | cds | g12296.t6.CDS4 | 22239432 | 22239646 |
| chr_1 | g12296 | g12296.t6 | TSS | g12296.t6 | NA | NA |
| chr_1 | g12296 | g12296.t6 | TTS | g12296.t6 | NA | NA |
Sequences
>g12296.t6 Gene=g12296 Length=2786
GAAATTTTCTGTATTTATGGTGGAACACCGTTACCGCAAACTGTATGGAGTAAAAATGGG
AAGCCAATAGCTTGGAGCGATCGTATAACTCAAGGAAATTATGGAAAATCGTTAGTAATT
CGGCATACTAATTTAGATGATAAAGGTTCATACACATGCGATGTTTCAAATGGTGCTGGT
CAGCAACAATCGGCTACAATTAATCTCGATATTAAGGCTATTCCATACTTTACTGTTGAG
CCTGAGCCAGTGAATGCAGCTGAAGAAGAAACTATTGAATTCAAATGTGAAGCTTCAGGT
ATTCCTGAACCTGCAATTAAATGGATTCACAATGGTAAACCAATTGAAGAAGCTGCACCA
AATCCACGTCGAATTGTTTCAAAGAATAAAATCATTATTAGAAATCTCGAGAAAAAAGAT
ACTGGCAATTATGGTTGTAACGCTACAAATGCTCTCGGCTATGTTTATAAAGACGTTTAT
GTTAATGTTTTGGCATTACCACCAGAAATTGAAGAAGCACCAGGAAAAGAGGCAACTGTT
GATCTTCGTGATATTACACTCAACTGTAAAGTTTTTGGTGCACCTAAACCAAAAATAAAA
TGGATTCGTAATGGCCAAGAATTGACTGGCGGTCGCTATGAGATTCAAGAAAGTGGCAGT
TTACTTATCAAACAAGTTTTGTTTGGAGATGCTGGTGAATATATTTGTCATGCTGAGAAT
AAATTTGGTAAGAAAGAAGCTAACGGAACTCTGATTGTTTATGAACATACAAAGATTACT
GAAACGCCAATTGATTATGAAGTTGTAGCTAAACAATTGGCTACATTCCGCTGTAACGCT
GTCTCTGATCCATCACTGCCTCTCACAATTGAATGGTTATTTAATGATGAACCAATTGAT
TTTGATGCTCAAGCACGATTCACAAAATCAAGTGATCATTCGTTGACAATTTCAGACACA
ATTGAACTTGATTCTGGAACATATACATGTCTTGCAAGTACTGAACTCGATTCAGCGCAA
GCATCTGCTACATTAACTGTGCAAGATGCACCAAATGCTCCAAAATTAACTGGTACTGAA
TGTTATGAAGATTATGCGAAAATTTCATGGGAACCACAGGGTGACAATCGTTCGCCAATT
TTATATTTCATTATTCAATATAATACATCATTTACACCTGCAACATGGGCAGATGCATCT
ACTCAAGTTCCTGCAACTGATTTCTCTTACACCGTTGATATGAGTCCATGGGGAAATTAT
ACTTTCCGTGTTATTGCAGTTAATAAAGTTGGCCCTTCAGCACCATCAGAACATAGTGAT
TCATGCAGCACACCACCAAAAGTTCCAGCCAAAAATCCTGATAATGTTGAAGGCAAAGGC
ACTGAGCCAAATAATCTCGTTATCAAATGGTCACCAATGCCTGAAATTGATCATAATGCT
CCACAATTTCACTACCGTGTCTCATGGAAACGCGATGTTGCTGGTGCAGAATGGCAGAAA
CGTGACATTCACGATTGGCAAAAAGGTGAGTTGCTTATACCAGATCAACCGACATTCCAA
CGTTATAAGATCAGAGTCCAAGCTGTAAATGAAAAAGGTGAAGCAGCAGTCGCAGTGAAA
GAAGTTGAAGGCTATTCCGGAGAAGACAAACCAACTGAAGCACCACAAAATTTCTCATTG
CATCAAATTGTCAGTGGAACTTCTGCAATGGTTTCCTGGAATGAAGTCTCACCTGAATCA
ATTCGTGGTCATTTCCGAGGCTACAAAATTCAAACATGGGTTGAAGGCGATGAAGACAAT
GTTAAGGAAATTCTGATGAAGAGTCAAACTTCGAAAGCACTTGTTGATAAATTTACTCCA
GATTCAACAAACTATGCTCGCATCATGGCATTTAATGATCGCTTTAATGGGCCACCTAGC
AATACTATTCAATTTGATACACCTGAAGGTGTACCAAGTACAGTTCAGTCACTGCAAGCT
TATCCTATGGGATCATCTGCTTTTTGGCTCACATGGAAGAGGCCATTATTAACAAATGGA
AAGTTGCGTGGTTATCGTATCTATTATGAAATTGTGAAAGGAACAGAACTTGAAGCGAGA
CAAGAAAGAGAGCCAAGAATTGAAAATCCAGATCAAAAATCTGCTAAACTTGCTGGCTTG
AAACCTAACACGAAATATCGTATTCACATTGTTGGCTTTACAAAAATGGGAGAAGGAGAA
GATTATTACATTGAAGCTACAACAGGAGCCGCTAGAACTGACGGTATTATAATTCCTAAA
CCAGATGTTCCTTCATTTGATTATGAACAACTTCCATCTGAAAATGGATATTCTAAAGTT
AAGGTCCATTGGAGACCAAATATTTCTGGAGATAAGCCTGGTTCACAGTTCTATGTAAAA
TATCGCGAACAAGGAGCATCAACTTGGTTGAAAGGAGACGATCGAATCAATGAAGATTTT
GCTGAAGTTGGAGGTTTAGAATCAGACAAGGTTTATGAATTCCGCGTTGTTTCTGTTGAT
GGTGATGAGCAAACAGAAAGTGCCTCGAAACTTATTGAGGGTTCATCAGATGGAGTAAGA
ATCAGACCTCCAGGTGATAATGGAATTGCGACAGCTGGTTGGTTTATTGGAATGCTTCTC
GCTCTTGCATTCCTTATTCTACTTTTGGTAATCATCTGCATCATTAAGCGTAATCGTGGT
GGCAAGTACGATGTTCATGATAGAGAACTCGCTAATGGACGACAAGATTACCCTGATGAA
GGCGGTTTTCATGAATATTCTCAACC
>g12296.t6 Gene=g12296 Length=515
MSPWGNYTFRVIAVNKVGPSAPSEHSDSCSTPPKVPAKNPDNVEGKGTEPNNLVIKWSPM
PEIDHNAPQFHYRVSWKRDVAGAEWQKRDIHDWQKGELLIPDQPTFQRYKIRVQAVNEKG
EAAVAVKEVEGYSGEDKPTEAPQNFSLHQIVSGTSAMVSWNEVSPESIRGHFRGYKIQTW
VEGDEDNVKEILMKSQTSKALVDKFTPDSTNYARIMAFNDRFNGPPSNTIQFDTPEGVPS
TVQSLQAYPMGSSAFWLTWKRPLLTNGKLRGYRIYYEIVKGTELEARQEREPRIENPDQK
SAKLAGLKPNTKYRIHIVGFTKMGEGEDYYIEATTGAARTDGIIIPKPDVPSFDYEQLPS
ENGYSKVKVHWRPNISGDKPGSQFYVKYREQGASTWLKGDDRINEDFAEVGGLESDKVYE
FRVVSVDGDEQTESASKLIEGSSDGVRIRPPGDNGIATAGWFIGMLLALAFLILLLVIIC
IIKRNRGGKYDVHDRELANGRQDYPDEGGFHEYSQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 20 | g12296.t6 | CDD | cd00063 | FN3 | 2 | 26 | 0.00161761 |
| 18 | g12296.t6 | CDD | cd00063 | FN3 | 39 | 121 | 6.0624E-8 |
| 19 | g12296.t6 | CDD | cd00063 | FN3 | 140 | 234 | 2.56965E-9 |
| 22 | g12296.t6 | CDD | cd00063 | FN3 | 239 | 327 | 1.57059E-12 |
| 21 | g12296.t6 | CDD | cd00063 | FN3 | 360 | 436 | 1.57875E-6 |
| 13 | g12296.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 35 | 1.5E-5 |
| 10 | g12296.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 36 | 134 | 4.4E-24 |
| 14 | g12296.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 135 | 231 | 4.2E-17 |
| 11 | g12296.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 232 | 342 | 8.8E-18 |
| 12 | g12296.t6 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 352 | 439 | 5.5E-8 |
| 28 | g12296.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 18 | 48 | - |
| 29 | g12296.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 21 | 35 | - |
| 5 | g12296.t6 | PANTHER | PTHR13817 | TITIN | 1 | 515 | 1.6E-153 |
| 6 | g12296.t6 | PANTHER | PTHR13817:SF122 | NEUROGLIAN | 1 | 515 | 1.6E-153 |
| 1 | g12296.t6 | Pfam | PF00041 | Fibronectin type III domain | 39 | 121 | 4.8E-7 |
| 4 | g12296.t6 | Pfam | PF00041 | Fibronectin type III domain | 141 | 227 | 3.8E-10 |
| 2 | g12296.t6 | Pfam | PF00041 | Fibronectin type III domain | 241 | 327 | 1.6E-10 |
| 3 | g12296.t6 | Pfam | PF00041 | Fibronectin type III domain | 361 | 429 | 1.7E-6 |
| 16 | g12296.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 458 | - |
| 17 | g12296.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 459 | 482 | - |
| 15 | g12296.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 483 | 515 | - |
| 33 | g12296.t6 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 1 | 34 | 11.409 |
| 30 | g12296.t6 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 39 | 136 | 16.907 |
| 31 | g12296.t6 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 141 | 237 | 16.836 |
| 34 | g12296.t6 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 238 | 340 | 16.087 |
| 32 | g12296.t6 | ProSiteProfiles | PS50853 | Fibronectin type-III domain profile. | 351 | 451 | 9.973 |
| 24 | g12296.t6 | SMART | SM00060 | FN3_2 | 36 | 122 | 0.0034 |
| 26 | g12296.t6 | SMART | SM00060 | FN3_2 | 139 | 224 | 0.37 |
| 25 | g12296.t6 | SMART | SM00060 | FN3_2 | 239 | 326 | 4.6E-9 |
| 27 | g12296.t6 | SMART | SM00060 | FN3_2 | 348 | 434 | 0.0025 |
| 9 | g12296.t6 | SUPERFAMILY | SSF49265 | Fibronectin type III | 2 | 122 | 8.74E-17 |
| 7 | g12296.t6 | SUPERFAMILY | SSF49265 | Fibronectin type III | 141 | 327 | 6.99E-29 |
| 8 | g12296.t6 | SUPERFAMILY | SSF49265 | Fibronectin type III | 346 | 430 | 3.38E-8 |
| 23 | g12296.t6 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 457 | 479 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
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.
