Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Hematopoietic lineage cell-specific protein.

Parent gene

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.t7 TTS g16588.t7 10120630 10120630
chr_4 g16588 g16588.t7 isoform g16588.t7 10120761 10122308
chr_4 g16588 g16588.t7 exon g16588.t7.exon1 10120761 10120862
chr_4 g16588 g16588.t7 cds g16588.t7.CDS1 10120761 10120862
chr_4 g16588 g16588.t7 exon g16588.t7.exon2 10121263 10121391
chr_4 g16588 g16588.t7 cds g16588.t7.CDS2 10121263 10121391
chr_4 g16588 g16588.t7 exon g16588.t7.exon3 10121446 10121927
chr_4 g16588 g16588.t7 cds g16588.t7.CDS3 10121446 10121927
chr_4 g16588 g16588.t7 exon g16588.t7.exon4 10121987 10122072
chr_4 g16588 g16588.t7 cds g16588.t7.CDS4 10121987 10122072
chr_4 g16588 g16588.t7 exon g16588.t7.exon5 10122144 10122234
chr_4 g16588 g16588.t7 cds g16588.t7.CDS5 10122144 10122234
chr_4 g16588 g16588.t7 exon g16588.t7.exon6 10122296 10122308
chr_4 g16588 g16588.t7 cds g16588.t7.CDS6 10122296 10122308
chr_4 g16588 g16588.t7 TSS g16588.t7 10122452 10122452

Sequences

>g16588.t7 Gene=g16588 Length=903
ATGTCTTACGATGATGATTGGGAAACTGACGCATCTTATGAAAATAAAATAACAGAAGAT
GAACAACGTTGGGGAAAAGGAGTCGATCGTGGTGCTGCAATTGACATGCAAAAGTTGATT
GAAGAAACTGAAAAAGCAGACGAAGAGAAAAAGAAGAAATTAGTTGAAACCGGCATTACT
GGATCGCATGGGTATGGAGGAAAATTTGGAGTACAAAAGGACAGAATGGATAAATCTGCT
TTAGGTCATGATTACATTGGAAAAGTAGAAAAGCATGGAAGTCAAAAAGACTATACAGGT
GGATTTGGTGGCAAATTTGGTGTTGACAAAGATCGCATGGATAAATCAGCAGTTGGATTT
GATTATGTCGGAAAAGTTGAAAAACATGACAGTCAAGCTGATTATAAAAAAGGTTTTGGT
GGTAAATTTGGACTTGAAACTGATAGAATGGACAAATCAGCTCATACATTTCAAGAACAA
GTTGACAAAGTTGGCACAAATTATCAAAAAATCAAGCCAGACATTTCTGGTGCAAAACCA
TCGAATTTGAAATCCAGATTTGAAAATATGGCGATTCATTCAGAAGAAGAGACGAAACAA
CGTGCTGCAATTCAAAAGAAATTGAGAGAAGAAAAAGATTTAATTGATAAACAACAAGCT
GCCAAAGAACATACTGTTGAGGAAGCAACAAAGGAAGTGACGAGAAAAACTGCGATAGTG
ACAGGAAGAAATGAAAAAATTAGCAATGTTATCAATGTTTTTAATGCACCACCACCAAGT
GATGAATTTAAACCAGCTCCGAATTTGGAAGGATTGGATAGTGAAGTTTCAAGCGATGAA
GAAGAAGGAAATGTCGATAAAGAAGAAACAAATAATTTTGATGAAGAAACAAAAAAATTT
GAT

>g16588.t7 Gene=g16588 Length=301
MSYDDDWETDASYENKITEDEQRWGKGVDRGAAIDMQKLIEETEKADEEKKKKLVETGIT
GSHGYGGKFGVQKDRMDKSALGHDYIGKVEKHGSQKDYTGGFGGKFGVDKDRMDKSAVGF
DYVGKVEKHDSQADYKKGFGGKFGLETDRMDKSAHTFQEQVDKVGTNYQKIKPDISGAKP
SNLKSRFENMAIHSEEETKQRAAIQKKLREEKDLIDKQQAAKEHTVEEATKEVTRKTAIV
TGRNEKISNVINVFNAPPPSDEFKPAPNLEGLDSEVSSDEEEGNVDKEETNNFDEETKKF
D

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16588.t7 Coils Coil Coil 36 56 -
10 g16588.t7 Coils Coil Coil 201 221 -
8 g16588.t7 MobiDBLite mobidb-lite consensus disorder prediction 255 301 -
9 g16588.t7 MobiDBLite mobidb-lite consensus disorder prediction 274 289 -
5 g16588.t7 PANTHER PTHR10829:SF5 HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN 4 112 8.6E-71
7 g16588.t7 PANTHER PTHR10829 CORTACTIN AND DREBRIN 4 112 8.6E-71
4 g16588.t7 PANTHER PTHR10829:SF5 HEMATOPOIETIC LINEAGE CELL-SPECIFIC PROTEIN 90 292 8.6E-71
6 g16588.t7 PANTHER PTHR10829 CORTACTIN AND DREBRIN 90 292 8.6E-71
3 g16588.t7 Pfam PF02218 Repeat in HS1/Cortactin 64 98 1.6E-19
1 g16588.t7 Pfam PF02218 Repeat in HS1/Cortactin 101 135 8.2E-19
2 g16588.t7 Pfam PF02218 Repeat in HS1/Cortactin 138 160 5.2E-9
12 g16588.t7 ProSiteProfiles PS51090 Cortactin repeat profile. 61 97 19.135
13 g16588.t7 ProSiteProfiles PS51090 Cortactin repeat profile. 98 134 19.633
14 g16588.t7 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

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.

Raw TPM values