General information for g16588.t5
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.t5 | TTS | g16588.t5 | 10119374 | 10119374 |
| chr_4 | g16588 | g16588.t5 | isoform | g16588.t5 | 10120271 | 10122308 |
| chr_4 | g16588 | g16588.t5 | exon | g16588.t5.exon1 | 10120271 | 10120366 |
| chr_4 | g16588 | g16588.t5 | cds | g16588.t5.CDS1 | 10120271 | 10120366 |
| chr_4 | g16588 | g16588.t5 | exon | g16588.t5.exon2 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t5 | cds | g16588.t5.CDS2 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t5 | exon | g16588.t5.exon3 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t5 | cds | g16588.t5.CDS3 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t5 | exon | g16588.t5.exon4 | 10121987 | 10122308 |
| chr_4 | g16588 | g16588.t5 | cds | g16588.t5.CDS4 | 10121987 | 10122071 |
| chr_4 | g16588 | g16588.t5 | TSS | g16588.t5 | 10122452 | 10122452 |
Sequences
>g16588.t5 Gene=g16588 Length=1029
ATGTCTTACGATGGTAAAAATTAAAAAAACTCAAAATTTCTTAAGTGAAAAATTTCATAA
AAATTATTTTCTAGATGATTGGGAAACTGACGCATCTTATGAAAATAAAATAACAGAAGA
TGAACAACGTTGGGGAAAAGGAGTCGATCGTGGTGCTGCAATTGAGTAAGTTAATTGAAA
AATTGATAAAAATTTCTTTAAACATTTTTATGATGATTCACTCGTACATTTTTTAGCATG
CAAAAGTTGATTGAAGAAACTGAAAAAGCAGACGAAGAGAAAAAGAAGAAATTAGTTGAA
ACCGGCATTACTGGATCGCATGGGTATGGAGGAAAATTTGGAGTACAAAAGGACAGAATG
GATAAATCTGCTTTAGGTCATGATTACATTGGAAAAGTAGAAAAGCATGGAAGTCAAAAA
GACTATACAGGTGGATTTGGTGGCAAATTTGGTGTTGACAAAGATCGCATGGATAAATCA
GCAGTTGGATTTGATTATGTCGGAAAAGTTGAAAAACATGACAGTCAAGCTGATTATAAA
AAAGGTTTTGGTGGTAAATTTGGACTTGAAACTGATAGAATGGACAAATCAGCTCATACA
TTTCAAGAACAAGTTGACAAAGTTGGCACAAATTATCAAAAAATCAAGCCAGACATTTCT
GGTGCAAAACCATCGAATTTGAAATCCAGATTTGAAAATATGGCGATTCATTCAGAAGAA
GAGACGAAACAACGTGCTGCAATTCAAAAGAAATTGAGAGAAGAAAAAGATTTAATTGAT
AAACAACAAGCTGCCAAAGAACATACTGTTGAGGAAGCAACAAAGGAAGTGACGAGAAAA
ACTGCGATAGTGACAGGAAGAAATGAAAAAATTAGCAATGTTATCAATGTTTTTAATGCA
CCACCACCAAGTGATGAATTTAAACCAGCTCCGAAACAACCAATAAAGCTCCCAAAAGAA
ACCAAACCAGCAGAGCCTGTGGAAATTGTGAAACCCGATATAATTTCAAGCACAGAAAAA
CATCTCGAT
>g16588.t5 Gene=g16588 Length=264
MQKLIEETEKADEEKKKKLVETGITGSHGYGGKFGVQKDRMDKSALGHDYIGKVEKHGSQ
KDYTGGFGGKFGVDKDRMDKSAVGFDYVGKVEKHDSQADYKKGFGGKFGLETDRMDKSAH
TFQEQVDKVGTNYQKIKPDISGAKPSNLKSRFENMAIHSEEETKQRAAIQKKLREEKDLI
DKQQAAKEHTVEEATKEVTRKTAIVTGRNEKISNVINVFNAPPPSDEFKPAPKQPIKLPK
ETKPAEPVEIVKPDIISSTEKHLD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16588.t5 | Coils | Coil | Coil | 1 | 21 | - |
| 12 | g16588.t5 | Coils | Coil | Coil | 166 | 186 | - |
| 10 | g16588.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 9 | g16588.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 223 | 264 | - |
| 8 | g16588.t5 | MobiDBLite | mobidb-lite | consensus disorder prediction | 233 | 248 | - |
| 4 | g16588.t5 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 26 | 63 | 3.7E-62 |
| 6 | g16588.t5 | PANTHER | PTHR10829:SF23 | CORTACTIN, ISOFORM A | 26 | 63 | 3.7E-62 |
| 5 | g16588.t5 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 27 | 249 | 3.7E-62 |
| 7 | g16588.t5 | PANTHER | PTHR10829:SF23 | CORTACTIN, ISOFORM A | 27 | 249 | 3.7E-62 |
| 3 | g16588.t5 | Pfam | PF02218 | Repeat in HS1/Cortactin | 29 | 63 | 1.3E-19 |
| 2 | g16588.t5 | Pfam | PF02218 | Repeat in HS1/Cortactin | 66 | 100 | 6.8E-19 |
| 1 | g16588.t5 | Pfam | PF02218 | Repeat in HS1/Cortactin | 103 | 125 | 4.4E-9 |
| 15 | g16588.t5 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 26 | 62 | 19.135 |
| 14 | g16588.t5 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 63 | 99 | 19.633 |
| 13 | g16588.t5 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 100 | 122 | 11.732 |
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 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.
