General information for g16588.t9
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Hematopoietic lineage cell-specific protein.
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.t9 | TTS | g16588.t9 | 10120630 | 10120630 |
| chr_4 | g16588 | g16588.t9 | isoform | g16588.t9 | 10121189 | 10122308 |
| chr_4 | g16588 | g16588.t9 | exon | g16588.t9.exon1 | 10121189 | 10121391 |
| chr_4 | g16588 | g16588.t9 | cds | g16588.t9.CDS1 | 10121248 | 10121391 |
| chr_4 | g16588 | g16588.t9 | exon | g16588.t9.exon2 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t9 | cds | g16588.t9.CDS2 | 10121446 | 10121927 |
| chr_4 | g16588 | g16588.t9 | exon | g16588.t9.exon3 | 10121987 | 10122072 |
| chr_4 | g16588 | g16588.t9 | cds | g16588.t9.CDS3 | 10121987 | 10122072 |
| chr_4 | g16588 | g16588.t9 | exon | g16588.t9.exon4 | 10122144 | 10122234 |
| chr_4 | g16588 | g16588.t9 | cds | g16588.t9.CDS4 | 10122144 | 10122234 |
| chr_4 | g16588 | g16588.t9 | exon | g16588.t9.exon5 | 10122296 | 10122308 |
| chr_4 | g16588 | g16588.t9 | cds | g16588.t9.CDS5 | 10122296 | 10122308 |
| chr_4 | g16588 | g16588.t9 | TSS | g16588.t9 | 10122452 | 10122452 |
Sequences
>g16588.t9 Gene=g16588 Length=875
ATGTCTTACGATGATGATTGGGAAACTGACGCATCTTATGAAAATAAAATAACAGAAGAT
GAACAACGTTGGGGAAAAGGAGTCGATCGTGGTGCTGCAATTGACATGCAAAAGTTGATT
GAAGAAACTGAAAAAGCAGACGAAGAGAAAAAGAAGAAATTAGTTGAAACCGGCATTACT
GGATCGCATGGGTATGGAGGAAAATTTGGAGTACAAAAGGACAGAATGGATAAATCTGCT
TTAGGTCATGATTACATTGGAAAAGTAGAAAAGCATGGAAGTCAAAAAGACTATACAGGT
GGATTTGGTGGCAAATTTGGTGTTGACAAAGATCGCATGGATAAATCAGCAGTTGGATTT
GATTATGTCGGAAAAGTTGAAAAACATGACAGTCAAGCTGATTATAAAAAAGGTTTTGGT
GGTAAATTTGGACTTGAAACTGATAGAATGGACAAATCAGCTCATACATTTCAAGAACAA
GTTGACAAAGTTGGCACAAATTATCAAAAAATCAAGCCAGACATTTCTGGTGCAAAACCA
TCGAATTTGAAATCCAGATTTGAAAATATGGCGATTCATTCAGAAGAAGAGACGAAACAA
CGTGCTGCAATTCAAAAGAAATTGAGAGAAGAAAAAGATTTAATTGATAAACAACAAGCT
GCCAAAGAACATACTGTTGAGGAAGCAACAAAGGAAGTGACGAGAAAAACTGCGATAGTG
ACAGGAAGAAATGAAAAAATTAGCAATGTTATCAATGTTTTTAATGCACCACCACCAAGT
GATGAATTTAAACCAGCTCCGGTGAGTAAAAATTGATGATTGTTGAAGTGAATTTTTGTT
AATTTGTTTTAGAAATTTCATAGTGATTAAATAAA
>g16588.t9 Gene=g16588 Length=271
MSYDDDWETDASYENKITEDEQRWGKGVDRGAAIDMQKLIEETEKADEEKKKKLVETGIT
GSHGYGGKFGVQKDRMDKSALGHDYIGKVEKHGSQKDYTGGFGGKFGVDKDRMDKSAVGF
DYVGKVEKHDSQADYKKGFGGKFGLETDRMDKSAHTFQEQVDKVGTNYQKIKPDISGAKP
SNLKSRFENMAIHSEEETKQRAAIQKKLREEKDLIDKQQAAKEHTVEEATKEVTRKTAIV
TGRNEKISNVINVFNAPPPSDEFKPAPVSKN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g16588.t9 | Coils | Coil | Coil | 36 | 56 | - |
| 8 | g16588.t9 | Coils | Coil | Coil | 201 | 221 | - |
| 5 | g16588.t9 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 4 | 98 | 8.9E-62 |
| 7 | g16588.t9 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 4 | 98 | 8.9E-62 |
| 4 | g16588.t9 | PANTHER | PTHR10829:SF5 | HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN | 90 | 233 | 8.9E-62 |
| 6 | g16588.t9 | PANTHER | PTHR10829 | CORTACTIN AND DREBRIN | 90 | 233 | 8.9E-62 |
| 3 | g16588.t9 | Pfam | PF02218 | Repeat in HS1/Cortactin | 64 | 98 | 1.4E-19 |
| 1 | g16588.t9 | Pfam | PF02218 | Repeat in HS1/Cortactin | 101 | 135 | 7.1E-19 |
| 2 | g16588.t9 | Pfam | PF02218 | Repeat in HS1/Cortactin | 138 | 160 | 4.5E-9 |
| 10 | g16588.t9 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 61 | 97 | 19.135 |
| 11 | g16588.t9 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 98 | 134 | 19.633 |
| 12 | g16588.t9 | ProSiteProfiles | PS51090 | Cortactin repeat profile. | 135 | 157 | 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 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.
