General information for g16446.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Beta-parvin.
Parent gene
- The parent gene g16446 is located on chr_4: 9466796..9467595 (- 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_4 | g16446 | g16446.t3 | isoform | g16446.t3 | 9465648 | 9467412 |
| chr_4 | g16446 | g16446.t3 | exon | g16446.t3.exon1 | 9465648 | 9466645 |
| chr_4 | g16446 | g16446.t3 | TTS | g16446.t3 | 9465650 | 9465650 |
| chr_4 | g16446 | g16446.t3 | cds | g16446.t3.CDS1 | 9466210 | 9466645 |
| chr_4 | g16446 | g16446.t3 | exon | g16446.t3.exon2 | 9466792 | 9466976 |
| chr_4 | g16446 | g16446.t3 | cds | g16446.t3.CDS2 | 9466792 | 9466976 |
| chr_4 | g16446 | g16446.t3 | exon | g16446.t3.exon3 | 9467051 | 9467412 |
| chr_4 | g16446 | g16446.t3 | cds | g16446.t3.CDS3 | 9467051 | 9467365 |
| chr_4 | g16446 | g16446.t3 | TSS | g16446.t3 | 9467762 | 9467762 |
Sequences
>g16446.t3 Gene=g16446 Length=1545
TTCAAGAAGTTCAAGAGGAAGGAAAATATGCAATTGATTCACCGGGAATGCCAAATGCTC
CAGAAATTCCACCAGAAGATTACAATTTAGAAGACAATGAGCAAAGATCAATAATTCAAC
CTCAATGTTTGAATCTTCCACAAGTTCGAGATTTATTGCAGTTGTTGATTGACTGGATCA
ATGATGAATTGGTTGAAGAGAGAATTATTGTGACAAATATTGAGCAAGATTTGTATGATG
GACAAGTTTTGCATAAATTATGGGAAAAATTGACAGGAAATAAATTGAATGTTTTGGAAG
TGACACAAAGTGAAGAAGGACAGAAGCAAAAATTGTCAGTTGTTTTAAATGCTGTCAATC
ATACTCTTGGATTTCATCATACAATGCCAAAATGGACAGTTGAAAGTGTTCATTCTAAAA
ATATTGTTGCAATTTTGCATCTTCTTGTTGCACTTGTTCGTCATTTTCGAGCTCCAATTC
GTCTTCCTGAAAATGTTTCTGTCACTGTTGTTGTTGTTAAAAAAAGTGGAACAAAATTAA
CTGCTGAAAAATTTGAAGAACAAATAACAACAACTTACGACGATGTTGGAATGAAATGTG
AACGTGATGCTTTCGATACACTTTTTGATCATGCACCAGAAAAATTACAAGTTGTTAAAA
AATCTCTTGTGACATTTGTCAACAAACATTTGAACAAACTCAATTTTGAAGTTGTCGATT
TGAGCACTGATTTTAGAGATGGAGTTTATTTGTGCCTTTTGATGGGATTACTTGGTGGAT
TTTTTGTGCCACTTCATGAATTTCATCTTACACCGAAAGATCAAGATCAAATGATACATA
ATGTTGCATTTTCATTTGATTTGATGCAAGATGTTGGTTTGGCAAAACCTAAAGCTAGAC
CAGAAGATATTGTCAATGCTGACATGAAATCAACACTTCGCTGCCTTTATAATCTCTTTA
CTAAATATAGAAACATCGCCTAAAAATTTGTCAAAAAGTGAAAAAAGAAATTAACAAAGA
ATTAATTGACGATTTAGTATTAATGAAAATTTTACTTAAAAATGTTGTTTGTGCCTTAAA
TGTTTTAATTTAAAAAATCTCAAGTGGAAGGATTATTGAACAAAGGAAATTTGGAATTTA
TTAAGTAGAATAAGACCAATGTTGAAAAAATACCAACTGCAACTTCAAAATCTTTGTGAT
GGCTACTTTTGAAAAAACTTTAAATTAGCCAATATCTACTGTAATTAATGCCATACAGCT
ACAGATCGATTGAATAACAACTCTTCATAATATTTGACACAAGAAATGAGAAATTTGTCA
AAAAACTGTTTGATAATTTGCATGAAATGCCTGGCATATAAAATTGATAATTTCAATGTA
TATTTTTTGTAAATTATCAAATTTTTCATATCTTGGTTTGACATGAGAAATTCAACTTGA
GAATAATTTTTGTTTTTTATTTACAAACTAACTGAAATTTAAAAGAAATTATTTTAATGA
AAACAGTCAAAGAAAAATAAAATATACTAATTTATTAATAAAAAT
>g16446.t3 Gene=g16446 Length=311
MPNAPEIPPEDYNLEDNEQRSIIQPQCLNLPQVRDLLQLLIDWINDELVEERIIVTNIEQ
DLYDGQVLHKLWEKLTGNKLNVLEVTQSEEGQKQKLSVVLNAVNHTLGFHHTMPKWTVES
VHSKNIVAILHLLVALVRHFRAPIRLPENVSVTVVVVKKSGTKLTAEKFEEQITTTYDDV
GMKCERDAFDTLFDHAPEKLQVVKKSLVTFVNKHLNKLNFEVVDLSTDFRDGVYLCLLMG
LLGGFFVPLHEFHLTPKDQDQMIHNVAFSFDLMQDVGLAKPKARPEDIVNADMKSTLRCL
YNLFTKYRNIA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g16446.t3 | Gene3D | G3DSA:1.10.418.10 | - | 18 | 142 | 7.5E-17 |
| 7 | g16446.t3 | Gene3D | G3DSA:1.10.418.10 | - | 180 | 311 | 1.6E-34 |
| 3 | g16446.t3 | PANTHER | PTHR12114:SF7 | BETA-PARVIN | 2 | 310 | 1.7E-135 |
| 4 | g16446.t3 | PANTHER | PTHR12114 | PARVIN | 2 | 310 | 1.7E-135 |
| 11 | g16446.t3 | PIRSF | PIRSF039131 | Parvin | 1 | 311 | 4.5E-159 |
| 2 | g16446.t3 | Pfam | PF00307 | Calponin homology (CH) domain | 39 | 141 | 1.8E-15 |
| 1 | g16446.t3 | Pfam | PF00307 | Calponin homology (CH) domain | 202 | 308 | 7.3E-17 |
| 9 | g16446.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 231 | - |
| 10 | g16446.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 232 | 249 | - |
| 8 | g16446.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 250 | 311 | - |
| 15 | g16446.t3 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 34 | 141 | 16.243 |
| 14 | g16446.t3 | ProSiteProfiles | PS50021 | Calponin homology (CH) domain profile. | 201 | 308 | 18.131 |
| 12 | g16446.t3 | SMART | SM00033 | ch_5 | 36 | 139 | 1.4 |
| 13 | g16446.t3 | SMART | SM00033 | ch_5 | 203 | 306 | 0.0094 |
| 5 | g16446.t3 | SUPERFAMILY | SSF47576 | Calponin-homology domain, CH-domain | 8 | 309 | 1.01E-42 |
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:0003779 | actin binding | MF |
| GO:0031532 | actin cytoskeleton reorganization | BP |
| GO:0007155 | cell adhesion | BP |
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K06275 (parvin)
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.
