General information for g16588.t2
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.t2 | TTS | g16588.t2 | 10119207 | 10119207 |
| chr_4 | g16588 | g16588.t2 | isoform | g16588.t2 | 10119728 | 10122308 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon1 | 10119728 | 10119898 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS1 | 10119728 | 10119898 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon2 | 10119956 | 10120366 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS2 | 10119956 | 10120366 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon3 | 10120761 | 10120862 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS3 | 10120761 | 10120862 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon4 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS4 | 10121263 | 10121391 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon5 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS5 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon6 | 10121987 | 10122072 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS6 | 10121987 | 10122072 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon7 | 10122144 | 10122234 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS7 | 10122144 | 10122234 |
| chr_4 | g16588 | g16588.t2 | exon | g16588.t2.exon8 | 10122296 | 10122308 |
| chr_4 | g16588 | g16588.t2 | cds | g16588.t2.CDS8 | 10122296 | 10122308 |
| chr_4 | g16588 | g16588.t2 | TSS | g16588.t2 | 10122452 | 10122452 |
Sequences
>g16588.t2 Gene=g16588 Length=1485
ATGTCTTACGATGATGATTGGGAAACTGACGCATCTTATGAAAATAAAATAACAGAAGAT
GAACAACGTTGGGGAAAAGGAGTCGATCGTGGTGCTGCAATTGACATGCAAAAGTTGATT
GAAGAAACTGAAAAAGCAGACGAAGAGAAAAAGAAGAAATTAGTTGAAACCGGCATTACT
GGATCGCATGGGTATGGAGGAAAATTTGGAGTACAAAAGGACAGAATGGATAAATCTGCT
TTAGGTCATGATTACATTGGAAAAGTAGAAAAGCATGGAAGTCAAAAAGACTATACAGGT
GGATTTGGTGGCAAATTTGGTGTTGACAAAGATCGCATGGATAAATCAGCAGTTGGATTT
GATTATGTCGGAAAAGTTGAAAAACATGACAGTCAAGCTGATTATAAAAAAGGTTTTGGT
GGTAAATTTGGACTTGAAACTGATAGAATGGACAAATCAGCTCATACATTTCAAGAACAA
GTTGACAAAGTTGGCACAAATTATCAAAAAATCAAGCCAGACATTTCTGGTGCAAAACCA
TCGAATTTGAAATCCAGATTTGAAAATATGGCGATTCATTCAGAAGAAGAGACGAAACAA
CGTGCTGCAATTCAAAAGAAATTGAGAGAAGAAAAAGATTTAATTGATAAACAACAAGCT
GCCAAAGAACATACTGTTGAGGAAGCAACAAAGGAAGTGACGAGAAAAACTGCGATAGTG
ACAGGAAGAAATGAAAAAATTAGCAATGTTATCAATGTTTTTAATGCACCACCACCAAGT
GATGAATTTAAACCAGCTCCGAATTTGGAAGGATTGGATAGTGAAGTTTCAAGCGATGAA
GAAGAAGGAAATGTCGATAAAGAAGAAACAAATAATTTTGATGAAGAAACAAAAAAATTT
GATAAACAACCAATAAAGCTCCCAAAAGAAACCAAACCAGCAGAGCCTGTGGAAATTGTG
AAACCCGATATAATTTCAAGCACAGAAAAACATCTCGATATGCCAGCACATCAAGGTGTT
TCAGCAATTGCTCAAAATTTCAGTCAACCAGCAGCACAATCACAACCTCAAAAACAAGAA
GAACAACAATCAGATATTCAAAGACATTCTGTTGAAGTTGTTCGTGAACCAGAAAGACAT
TCAAATGGAGTTAGTGAACAAAAAGTAGTTGAAGAAGTAGTTCAAAAAGTTCAAGAAATT
GCTGAACCTGAAGTGATAGAACAAGAACTAATAGAGCAGCTGAAAAATGATACAGTTGAG
CCAGTTGAAGAAGAAGAACAATTTGTGTTGTCACCTGATAACCCTGGAATTACTGCAATT
GCACTTTATGACTATCAAGCAGCAGCTGAAGATGAAATTTCTTTCGATCCTGATGATTTA
ATTACACATATTGACATGATTGATCCTGGTTGGTATAAAGGACTTCATGCAAAGACATAC
ACTTATGGCCTCTTTCCTGCAAATTATGTGCAAATTCAAGAGTAG
>g16588.t2 Gene=g16588 Length=494
MSYDDDWETDASYENKITEDEQRWGKGVDRGAAIDMQKLIEETEKADEEKKKKLVETGIT
GSHGYGGKFGVQKDRMDKSALGHDYIGKVEKHGSQKDYTGGFGGKFGVDKDRMDKSAVGF
DYVGKVEKHDSQADYKKGFGGKFGLETDRMDKSAHTFQEQVDKVGTNYQKIKPDISGAKP
SNLKSRFENMAIHSEEETKQRAAIQKKLREEKDLIDKQQAAKEHTVEEATKEVTRKTAIV
TGRNEKISNVINVFNAPPPSDEFKPAPNLEGLDSEVSSDEEEGNVDKEETNNFDEETKKF
DKQPIKLPKETKPAEPVEIVKPDIISSTEKHLDMPAHQGVSAIAQNFSQPAAQSQPQKQE
EQQSDIQRHSVEVVREPERHSNGVSEQKVVEEVVQKVQEIAEPEVIEQELIEQLKNDTVE
PVEEEEQFVLSPDNPGITAIALYDYQAAAEDEISFDPDDLITHIDMIDPGWYKGLHAKTY
TYGLFPANYVQIQE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g16588.t2 | Coils | Coil | Coil | 36 | 56 | - |
| 14 | g16588.t2 | Coils | Coil | Coil | 201 | 221 | - |
| 13 | g16588.t2 | Gene3D | G3DSA:2.30.30.40 | SH3 Domains | 422 | 494 | 1.8E-20 |
| 18 | g16588.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 257 | 320 | - |
| 20 | g16588.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 274 | 289 | - |
| 19 | g16588.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 290 | 317 | - |
| 17 | g16588.t2 | MobiDBLite | mobidb-lite | consensus disorder prediction | 349 | 368 | - |
| 6 | g16588.t2 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 4 | 112 | 2.3E-93 |
| 8 | g16588.t2 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 4 | 112 | 2.3E-93 |
| 5 | g16588.t2 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 90 | 493 | 2.3E-93 |
| 7 | g16588.t2 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 90 | 493 | 2.3E-93 |
| 11 | g16588.t2 | PRINTS | PR00452 | SH3 domain signature | 437 | 447 | 1.8E-5 |
| 9 | g16588.t2 | PRINTS | PR00452 | SH3 domain signature | 451 | 466 | 1.8E-5 |
| 10 | g16588.t2 | PRINTS | PR00452 | SH3 domain signature | 481 | 493 | 1.8E-5 |
| 4 | g16588.t2 | Pfam | PF02218 | Repeat in HS1/Cortactin | 64 | 98 | 3.0E-19 |
| 2 | g16588.t2 | Pfam | PF02218 | Repeat in HS1/Cortactin | 101 | 135 | 1.6E-18 |
| 3 | g16588.t2 | Pfam | PF02218 | Repeat in HS1/Cortactin | 138 | 160 | 7.2E-9 |
| 1 | g16588.t2 | Pfam | PF14604 | Variant SH3 domain | 441 | 491 | 2.7E-11 |
| 22 | g16588.t2 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 61 | 97 | 19.135 |
| 23 | g16588.t2 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 98 | 134 | 19.633 |
| 24 | g16588.t2 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 135 | 157 | 11.732 |
| 21 | g16588.t2 | ProSiteProfiles | PS50002 | Src homology 3 (SH3) domain profile. | 434 | 494 | 23.957 |
| 16 | g16588.t2 | SMART | SM00326 | SH3_2 | 437 | 494 | 7.0E-18 |
| 12 | g16588.t2 | SUPERFAMILY | SSF50044 | SH3-domain | 432 | 492 | 2.1E-18 |
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:0005515 | protein binding | MF |
| GO:0030041 | actin filament polymerization | BP |
KEGG
Orthology
- This transcript has been annotated with K06106 (cortactin)
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.
