Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Focal adhesion kinase 1.

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_2 g5835 g5835.t2 isoform g5835.t2 12211502 12212919
chr_2 g5835 g5835.t2 exon g5835.t2.exon1 12211502 12211964
chr_2 g5835 g5835.t2 cds g5835.t2.CDS1 12211504 12211964
chr_2 g5835 g5835.t2 exon g5835.t2.exon2 12212063 12212527
chr_2 g5835 g5835.t2 cds g5835.t2.CDS2 12212063 12212351
chr_2 g5835 g5835.t2 exon g5835.t2.exon3 12212833 12212919
chr_2 g5835 g5835.t2 TSS g5835.t2 12212954 12212954
chr_2 g5835 g5835.t2 TTS g5835.t2 NA NA

Sequences

>g5835.t2 Gene=g5835 Length=1015
AAAAAATAAAAAAGAAAATAAATTAAAATAAAATAGTTTCTCAGCTCAATATTCAATGAA
GTAATAAAAAAAATTGAGATCTAAATCAACTTCCATTTTTTCTCTTATTCATATAATTAA
TGCACAAATACCATACATAAGCAGCTTGCTGCAATAGCCACAGCGAGCGAGCTCATATTT
ATGAAAAAAGAATACAAGAGAAGAAGAAAATAAAATTGTAATAAAAGTGGATTTTGATAG
AGCGAGAAGGCGCAATTGAGATTATGGATGAATTAAGTGTTAATAGCAGGCACTTTAGTC
CAAACTTCAGTCCATCGAGAAATCTTGTAGGCAACAATAGCGAGAATCAGACACAAAAAT
CGCTTTACATTCATTTAGTTAATCATGGTTTTCGAATGGTTCGTGTAGATGATTCAAATA
GCGATGTAAGGCAAATTATAAGTAATGTTGTGGGATCGATGACAAGTCCTGTTGGTGTAA
AACCGTGTACGCAATTTTATGCATTACGACTCCGACATATTGTCTCCAAAGAAATTCTTT
GGCTGCCACTGTCGACACCGACACGACAAGTTATTGATTACATCTCAAATGAATCATGCT
CGAATATAAATTGTCCCAATTATGTGAGATCATCATCTCCATCAGCATCGTCATTGTGCG
ACAAGAGTCAGCAACAACAAGAGTCAAAAGAAAATGTACCTCTAGGCCATTCGAATTGTG
TATGGAAAATAGAATTACGTGTACGCTATATTCCAAAGAGTCTCAGTGAATTTCTTGAAC
GTGATAAAATAACCATCAACTTCTACTTTAATCAAGTGAAGGACGATTTTGTACAATCAA
ATATTGCGAGTATCGAGCAAGATTTGGCTGTACAATTGTGCTGTCTTGCGATACGACACT
ATTACAAGGACGCAAGATCGTCGAACGACAGAAAACATCATCTCGATTACATTGAAAAAG
AGATGGGTTTCTCAAATTTCCTGCCTAAAAGCGTAATCGATACGATAAAGCTAAA

>g5835.t2 Gene=g5835 Length=250
MDELSVNSRHFSPNFSPSRNLVGNNSENQTQKSLYIHLVNHGFRMVRVDDSNSDVRQIIS
NVVGSMTSPVGVKPCTQFYALRLRHIVSKEILWLPLSTPTRQVIDYISNESCSNINCPNY
VRSSSPSASSLCDKSQQQQESKENVPLGHSNCVWKIELRVRYIPKSLSEFLERDKITINF
YFNQVKDDFVQSNIASIEQDLAVQLCCLAIRHYYKDARSSNDRKHHLDYIEKEMGFSNFL
PKSVIDTIKL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g5835.t2 CDD cd14473 FERM_B-lobe 177 250 0.000000
6 g5835.t2 Gene3D G3DSA:3.10.20.90 - 20 112 0.000000
7 g5835.t2 Gene3D G3DSA:1.20.80.10 - 162 250 0.000000
2 g5835.t2 PANTHER PTHR46221:SF5 PROTEIN TYROSINE KINASE 2AA 28 249 0.000000
3 g5835.t2 PANTHER PTHR46221 FERM AND PDZ DOMAIN-CONTAINING PROTEIN FAMILY MEMBER 28 249 0.000000
1 g5835.t2 Pfam PF18038 FERM N-terminal domain 42 98 0.000036
8 g5835.t2 ProSiteProfiles PS50057 FERM domain profile. 32 250 22.386000
4 g5835.t2 SUPERFAMILY SSF54236 Ubiquitin-like 31 164 0.000000
5 g5835.t2 SUPERFAMILY SSF47031 Second domain of FERM 165 249 0.000000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5835/g5835.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5835.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005856 cytoskeleton CC

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.

Raw TPM values