General information for g16588.t8
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Src substrate cortactin.
Parent gene
- The parent gene g16588 is located on chr_4: 10121391..10122308 (- 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 | g16588 | g16588.t8 | TTS | g16588.t8 | 10120630 | 10120630 |
| chr_4 | g16588 | g16588.t8 | isoform | g16588.t8 | 10120761 | 10122308 |
| chr_4 | g16588 | g16588.t8 | exon | g16588.t8.exon1 | 10120761 | 10120862 |
| chr_4 | g16588 | g16588.t8 | cds | g16588.t8.CDS1 | 10120761 | 10120862 |
| chr_4 | g16588 | g16588.t8 | exon | g16588.t8.exon2 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t8 | cds | g16588.t8.CDS2 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t8 | exon | g16588.t8.exon3 | 10121446 | 10122308 |
| chr_4 | g16588 | g16588.t8 | cds | g16588.t8.CDS3 | 10121446 | 10121892 |
| chr_4 | g16588 | g16588.t8 | TSS | g16588.t8 | 10122452 | 10122452 |
Sequences
>g16588.t8 Gene=g16588 Length=1094
ATGTCTTACGATGGTAAAAATTAAAAAAACTCAAAATTTCTTAAGTGAAAAATTTCATAA
AAATTATTTTCTAGATGATTGGGAAACTGACGCATCTTATGAAAATAAAATAACAGAAGA
TGAACAACGTTGGGGAAAAGGAGTCGATCGTGGTGCTGCAATTGAGTAAGTTAATTGAAA
AATTGATAAAAATTTCTTTAAACATTTTTATGATGATTCACTCGTACATTTTTTAGCATG
CAAAAGTTGATTGAAGAAACTGAAAAAGCAGACGAAGAGAAAAAGAAGAAATTAGTTGAA
ACCGGCATTACTGGATCGCATGGTTGGTCCTCAAAATAATTTATAAAACAATAAATTTAA
AATTTTACCTTTTAATTTTAGGGTATGGAGGAAAATTTGGAGTACAAAAGGACAGAATGG
ATAAATCTGCTTTAGGTCATGATTACATTGGAAAAGTAGAAAAGCATGGAAGTCAAAAAG
ACTATACAGGTGGATTTGGTGGCAAATTTGGTGTTGACAAAGATCGCATGGATAAATCAG
CAGTTGGATTTGATTATGTCGGAAAAGTTGAAAAACATGACAGTCAAGCTGATTATAAAA
AAGGTTTTGGTGGTAAATTTGGACTTGAAACTGATAGAATGGACAAATCAGCTCATACAT
TTCAAGAACAAGTTGACAAAGTTGGCACAAATTATCAAAAAATCAAGCCAGACATTTCTG
GTGCAAAACCATCGAATTTGAAATCCAGATTTGAAAATATGGCGATTCATTCAGAAGAAG
AGACGAAACAACGTGCTGCAATTCAAAAGAAATTGAGAGAAGAAAAAGATTTAATTGATA
AACAACAAGCTGCCAAAGAACATACTGTTGAGGAAGCAACAAAGGAAGTGACGAGAAAAA
CTGCGATAGTGACAGGAAGAAATGAAAAAATTAGCAATGTTATCAATGTTTTTAATGCAC
CACCACCAAGTGATGAATTTAAACCAGCTCCGAATTTGGAAGGATTGGATAGTGAAGTTT
CAAGCGATGAAGAAGAAGGAAATGTCGATAAAGAAGAAACAAATAATTTTGATGAAGAAA
CAAAAAAATTTGAT
>g16588.t8 Gene=g16588 Length=226
MDKSALGHDYIGKVEKHGSQKDYTGGFGGKFGVDKDRMDKSAVGFDYVGKVEKHDSQADY
KKGFGGKFGLETDRMDKSAHTFQEQVDKVGTNYQKIKPDISGAKPSNLKSRFENMAIHSE
EETKQRAAIQKKLREEKDLIDKQQAAKEHTVEEATKEVTRKTAIVTGRNEKISNVINVFN
APPPSDEFKPAPNLEGLDSEVSSDEEEGNVDKEETNNFDEETKKFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g16588.t8 | Coils | Coil | Coil | 126 | 146 | - |
| 8 | g16588.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 180 | 226 | - |
| 9 | g16588.t8 | MobiDBLite | mobidb-lite | consensus disorder prediction | 199 | 214 | - |
| 4 | g16588.t8 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 1 | 37 | 3.5E-50 |
| 6 | g16588.t8 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 1 | 37 | 3.5E-50 |
| 5 | g16588.t8 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 15 | 217 | 3.5E-50 |
| 7 | g16588.t8 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 15 | 217 | 3.5E-50 |
| 3 | g16588.t8 | Pfam | PF02218 | Repeat in HS1/Cortactin | 1 | 23 | 6.5E-9 |
| 1 | g16588.t8 | Pfam | PF02218 | Repeat in HS1/Cortactin | 26 | 60 | 5.4E-19 |
| 2 | g16588.t8 | Pfam | PF02218 | Repeat in HS1/Cortactin | 63 | 85 | 3.6E-9 |
| 13 | g16588.t8 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 1 | 22 | 10.91 |
| 11 | g16588.t8 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 23 | 59 | 19.633 |
| 12 | g16588.t8 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 60 | 82 | 11.732 |
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:0030041 | actin filament polymerization | BP |
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.
