General information for g12288.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Homer protein homolog 2.
Parent gene
- The parent gene g12288 is located on chr_1: 22174122..22176469 (+ 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 | g12288 | g12288.t1 | isoform | g12288.t1 | 22174122 | 22176469 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon1 | 22174122 | 22174126 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS1 | 22174122 | 22174126 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon2 | 22174558 | 22174714 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS2 | 22174558 | 22174714 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon3 | 22174788 | 22174841 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS3 | 22174788 | 22174841 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon4 | 22174903 | 22175175 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS4 | 22174903 | 22175175 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon5 | 22175234 | 22175394 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS5 | 22175234 | 22175394 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon6 | 22175467 | 22175545 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS6 | 22175467 | 22175545 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon7 | 22175615 | 22175854 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS7 | 22175615 | 22175854 |
| chr_1 | g12288 | g12288.t1 | exon | g12288.t1.exon8 | 22176035 | 22176469 |
| chr_1 | g12288 | g12288.t1 | cds | g12288.t1.CDS8 | 22176035 | 22176469 |
| chr_1 | g12288 | g12288.t1 | TSS | g12288.t1 | NA | NA |
| chr_1 | g12288 | g12288.t1 | TTS | g12288.t1 | NA | NA |
Sequences
>g12288.t1 Gene=g12288 Length=1404
ATGGGCGAGCAACCGATATACATTTGCCAAGCTCATGTCTTTCACATAGACCCAAAAACA
AAACGTACATGGATAACAGCATCGAGTAAGGCAATTAGTGTAAGCTTCTTCTATGATTCT
TCAAGAAATCTCTATAGAATTATTTCTGTTGAGGGGACAAAGGCGGTTATCAATTCGACC
ATCACTCCAAATATGACATTCACTCAAACGTCTCAGAAATTCGGTCAATGGAGCGATGTT
CGGGCCAATACAGTTTATGGATTGGGATTTGCGAGTGAAGCGGAACTGGGGAAGTTTATA
GAAAAATTTCAGGAAGTCAAAGAGGCTACGAAAAATGCAATGGCAAAAGCAAATGCGAAT
GGAAGTTCCGCTGTAACGCCTGCCACAAGTGCAAATGCATCGCCTATAACATCAAGGTCA
TCGATAACACAAAATGATAGCTTTGTTTCTGATATTGCTGAACCACCATTAAGTGCATCT
GGTTCTGTTAAGAATGAAAGTCCACAACATTCAATATCAGCAAATAATAATAACACAATA
ACAAATGATCACAAAGGAGTTTCTAGCAACTCATCGACTGAAGGTGCACCAGGTTCAGAT
CAACAATTGAAATATGAAAATGAACGTTTAAAATTAGCATTAGCACAAAGCTCTGCGAAC
GCGAAGAAATGGGAAATTGAATTATCCACACTCAAGAGTAATAATTTACGTTTAACTAGT
GCTTTACAGGAATCGACAGCAAATGTTGATGAATGGAAACGCCAACTTCATGCATATAAA
GAAGAAAATCAGAGGCTGAAAGTGAGATTACAAGAATTAGAGAATTCAAAAGGTGGTGGA
AGTGGAAGTCTATCAAGTAGCGATGCATTAACAGATGATTTAAGAAGGGAAATTACTTTA
CTTAAAAGTCGCATCGAAGGTCTCGAAAAGGAGTTGATGAATCAGGAAGTTGAATTAAAA
GCGGCCAAAAATCATCAAAGCATTTTCTCTGAAGAAATTTACAATTCACTTCATAAACGT
GATCAAAATCTTCAAGTGGAAAAGGATAGTAATAATAATTCAACAATTAGTACCAAAGTC
AAACCGAAAATAGATAAGAATACAAGTAAGCCAAACGAAATAAACGAAACAATCACCACA
ACCATTAACAACATTTCAAAAGAAAAGAAAAGTGTTAAGATAACCGATCCGAAATCAATT
AACAACAATAATCTCGATAATTCTCAAGTACAGAATGCTACAAATACATTAAAAAGAAAA
CGTGAAGCAAAATCTCCCATTAAAACAGCCGATTCACCATCATCTGAAGAGATGAGCAAA
AAGCAGAGCAGTCAAACAACTGCAACAATTTTAGTATCAAAAACTAAAACAAAGTCTGGA
CTTCCATTACTTTTGAAGAAATGA
>g12288.t1 Gene=g12288 Length=467
MGEQPIYICQAHVFHIDPKTKRTWITASSKAISVSFFYDSSRNLYRIISVEGTKAVINST
ITPNMTFTQTSQKFGQWSDVRANTVYGLGFASEAELGKFIEKFQEVKEATKNAMAKANAN
GSSAVTPATSANASPITSRSSITQNDSFVSDIAEPPLSASGSVKNESPQHSISANNNNTI
TNDHKGVSSNSSTEGAPGSDQQLKYENERLKLALAQSSANAKKWEIELSTLKSNNLRLTS
ALQESTANVDEWKRQLHAYKEENQRLKVRLQELENSKGGGSGSLSSSDALTDDLRREITL
LKSRIEGLEKELMNQEVELKAAKNHQSIFSEEIYNSLHKRDQNLQVEKDSNNNSTISTKV
KPKIDKNTSKPNEINETITTTINNISKEKKSVKITDPKSINNNNLDNSQVQNATNTLKRK
REAKSPIKTADSPSSEEMSKKQSSQTTATILVSKTKTKSGLPLLLKK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g12288.t1 | CDD | cd01206 | EVH1_Homer_Vesl | 3 | 111 | 3.50281E-70 |
| 6 | g12288.t1 | Coils | Coil | Coil | 100 | 120 | - |
| 8 | g12288.t1 | Coils | Coil | Coil | 207 | 234 | - |
| 7 | g12288.t1 | Coils | Coil | Coil | 242 | 276 | - |
| 9 | g12288.t1 | Coils | Coil | Coil | 291 | 325 | - |
| 5 | g12288.t1 | Gene3D | G3DSA:2.30.29.30 | - | 1 | 115 | 9.4E-33 |
| 19 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 118 | 140 | - |
| 18 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 159 | 200 | - |
| 16 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 160 | 200 | - |
| 14 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 345 | 372 | - |
| 13 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 347 | 362 | - |
| 17 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 389 | 467 | - |
| 12 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 396 | 416 | - |
| 15 | g12288.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 428 | 456 | - |
| 2 | g12288.t1 | PANTHER | PTHR10918:SF5 | HOMER, ISOFORM E | 1 | 387 | 1.5E-136 |
| 3 | g12288.t1 | PANTHER | PTHR10918 | HOMER | 1 | 387 | 1.5E-136 |
| 1 | g12288.t1 | Pfam | PF00568 | WH1 domain | 4 | 106 | 2.1E-33 |
| 20 | g12288.t1 | ProSiteProfiles | PS50229 | WH1 domain profile. | 1 | 110 | 20.126 |
| 11 | g12288.t1 | SMART | SM00461 | WH1_2 | 1 | 107 | 4.7E-29 |
| 4 | g12288.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 1 | 129 | 6.37E-39 |
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:0035256 | G protein-coupled glutamate receptor binding | MF |
KEGG
Orthology
- This transcript has been annotated with K15010 (homer)
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.
