Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t1 TTS g5835.t1 12205800 12205800
chr_2 g5835 g5835.t1 isoform g5835.t1 12206680 12212351
chr_2 g5835 g5835.t1 exon g5835.t1.exon1 12206680 12207073
chr_2 g5835 g5835.t1 cds g5835.t1.CDS1 12206680 12207073
chr_2 g5835 g5835.t1 exon g5835.t1.exon2 12207132 12207242
chr_2 g5835 g5835.t1 cds g5835.t1.CDS2 12207132 12207242
chr_2 g5835 g5835.t1 exon g5835.t1.exon3 12207301 12207797
chr_2 g5835 g5835.t1 cds g5835.t1.CDS3 12207301 12207797
chr_2 g5835 g5835.t1 exon g5835.t1.exon4 12208017 12209502
chr_2 g5835 g5835.t1 cds g5835.t1.CDS4 12208017 12209502
chr_2 g5835 g5835.t1 exon g5835.t1.exon5 12209557 12209729
chr_2 g5835 g5835.t1 cds g5835.t1.CDS5 12209557 12209729
chr_2 g5835 g5835.t1 exon g5835.t1.exon6 12209799 12209830
chr_2 g5835 g5835.t1 cds g5835.t1.CDS6 12209799 12209830
chr_2 g5835 g5835.t1 exon g5835.t1.exon7 12209895 12209952
chr_2 g5835 g5835.t1 cds g5835.t1.CDS7 12209895 12209952
chr_2 g5835 g5835.t1 exon g5835.t1.exon8 12210013 12210092
chr_2 g5835 g5835.t1 cds g5835.t1.CDS8 12210013 12210092
chr_2 g5835 g5835.t1 exon g5835.t1.exon9 12210151 12210287
chr_2 g5835 g5835.t1 cds g5835.t1.CDS9 12210151 12210287
chr_2 g5835 g5835.t1 exon g5835.t1.exon10 12210359 12210491
chr_2 g5835 g5835.t1 cds g5835.t1.CDS10 12210359 12210491
chr_2 g5835 g5835.t1 exon g5835.t1.exon11 12210564 12211964
chr_2 g5835 g5835.t1 cds g5835.t1.CDS11 12210564 12211964
chr_2 g5835 g5835.t1 exon g5835.t1.exon12 12212063 12212351
chr_2 g5835 g5835.t1 cds g5835.t1.CDS12 12212063 12212351
chr_2 g5835 g5835.t1 TSS g5835.t1 12212954 12212954

Sequences

>g5835.t1 Gene=g5835 Length=4791
ATGGATGAATTAAGTGTTAATAGCAGGCACTTTAGTCCAAACTTCAGTCCATCGAGAAAT
CTTGTAGGCAACAATAGCGAGAATCAGACACAAAAATCGCTTTACATTCATTTAGTTAAT
CATGGTTTTCGAATGGTTCGTGTAGATGATTCAAATAGCGATGTAAGGCAAATTATAAGT
AATGTTGTGGGATCGATGACAAGTCCTGTTGGTGTAAAACCGTGTACGCAATTTTATGCA
TTACGACTCCGACATATTGTCTCCAAAGAAATTCTTTGGCTGCCACTGTCGACACCGACA
CGACAAGTTATTGATTACATCTCAAATGAATCATGCTCGAATATAAATTGTCCCAATTAT
GTGAGATCATCATCTCCATCAGCATCGTCATTGTGCGACAAGAGTCAGCAACAACAAGAG
TCAAAAGAAAATGTACCTCTAGGCCATTCGAATTGTGTATGGAAAATAGAATTACGTGTA
CGCTATATTCCAAAGAGTCTCAGTGAATTTCTTGAACGTGATAAAATAACCATCAACTTC
TACTTTAATCAAGTGAAGGACGATTTTGTACAATCAAATATTGCGAGTATCGAGCAAGAT
TTGGCTGTACAATTGTGCTGTCTTGCGATACGACACTATTACAAGGACGCAAGATCGTCG
AACGACAGAAAACATCATCTCGATTACATTGAAAAAGAGATGGGTTTCTCAAATTTCCTG
CCTAAAAGCGTAATCGATACGATAAAGCTAAAGAACTTAAAAAAACTTGTACAGTCACAA
TATAAGAAAATCTATCAACTATCAGATACTGATTACATCTTAAAGTACTTTGAATTACTC
TCGACTGTCTTTGACTTTGACCATGAGAAATTTGTTGTGACATTGGGACAATGGAACATT
GCAATTGACCTAATTATTGGCTACAACCTTGGAATCTCTTACTTGACGCATTCACAAGCA
AAACCAACAAAAGTGACCGATTTTGAGAACATTTTGTCACTAAAAACGAGCATTCTACCA
AACACACTACAGCAGTCATCAATATCAAGTGGAAGCACAAGTGGCAAAGGTTTACATAAT
AGTAAATCAAACGATTCAAACATTTCACAAGTAAGCTCGTTGTGTGGATGCAATAATATT
AAATCACAGTTGCGCATTCAGGTAGATGGAAATAGCGAGGACTTGGCAATAACATGCAAT
GGTGTAAATACTGCTGATGGCATAGCTGAACTTATTGACGGTTATTGTAAAATATTCAAT
GACAATAATGTCAGTTTATGGGATAAATCGAAAACACCCATCAATAGTAATTCATTAGAG
AAAAGAATGCCAGCGTATGTACAAAATAATGACAATGGTGGTGATGAAAATGAAATGAAC
TTAAGGAGAGTAATGTTGAGTGAAGATTATTCTGAATTGCATGGTGGTGTTTTACCAGAA
GTAGAAGAAGAAGGCGATTATTCAACGCCAACTGCTCGAAATTATGAACTTCAACGTAAT
CAAATTCAATTAAATGAGATTATTGGCATTGGACAATTTGGTGATGTTTATGTTGGTACA
TGTCAAATTATTAGATCTGCAAGCAAAAAAGATCCAACGACTGTCCGTGAAGATATTGTT
CCTGTGGCTGTTAAAACATGTAAAGCAGACGCGGATCTTAAAACCTCAGAGAAATTCCTT
GAAGAAGCATACGTAATGCAAAAATTTGAGCACCCACACATCATACGACTTATTGGTATC
TGCAGTGATCCGCCTATTTGGTTGGTGATGGAGCTTGCAAGATTGGGCGAATTGCGAGCA
TATTTGAAAGAAAACAGCTCTAAATTAAAGCTCGGCACATTGCTTTTATATTCTTATCAA
CTCTCAACTGCTTTAAGTTATTTAGAATCAAAAAAATTTGTTCATCGCGATATTGCAGCG
AGAAATGTTCTTGTCTCTAGTCCTACATGTATTAAATTAGCTGATTTTGGTTTATCAAGA
TGGGTCGAAGATCAATCATATTATACTTCCAGTAAAGGTCTTTTACCAATTAAATGGATG
GCACCAGAAAGTATAAATTTTCGTCGATTTACTACTGCTAGTGATGTGTGGATGTTTGCT
GTTTGTACGTGGGAAATTTTAATGTATGGCGTAAAACCTTTTCAAGGAATTAAAAATAGC
GAGGTAATAGGAAAATTAGAAAATGGTGAAAGACTTGCATTGCCGCCCAATTGTCCTCCA
CGACTTTATTCACTCATGTCACAATGTTGGAGTTATGAACCAGCGAAACGTCCAGATTTT
AAAACAATTAAAGAGATTATGAAAGAGATATTAATTGAAGAGAAAATCAGTGATTCAGAA
ACAATGAAGCGAGAAAATCGTAGAATTGCAGCAATGTCATGGGGTGCGGGTGATGAAGAT
GCACCACCGAAGCCAGCTCGACCTATGACAGATTCTACTTCAAAACTCTTCACCATTGAA
GATCGAAATGAAAATGGAACATCGAATAACAGTGGACCTCAAATGACTTACATCATTGCA
CAAAATCCAGCTGTTTTAGCTCAACTAATGCGTGAAAATGAGAAGAGAGGCTTAAATCCA
TCAGCTTATACAACACCTGCATCGGTATTTAACGTTCTAGCTGTCGATTTTGCAGAAGAT
GCTGCAGCTACTGAAAATAACGCCATCGATCAAGTTCAATTAAAGGCCATGCAAGTGCCA
GCAATGGAACTTATTCCATTGCAACAAGATAATACTAATGAAATCCTTGAACCTTCACCC
TCTCTCAATCAAATTCCAAATTTTGAAGCATTAGGTACGAATGTCGATATGTCTGTTGCT
TATCCTATTACATCACCATCTGGTTTACCACCTCAAGCGCCAATCGATAATTCAAAGACA
AGAAGTTTGGAGAGAAATGCTGGACAAAATGTTCCACCTTCTGTTTCAGCTCGAGTTAGT
TCACTTGAAAGAAGACAACAGATTCAAGAAAATCTCAAAGGTAATCAACAACGATCTCAG
TCATTGATAAGACAATATAGTGCTGGTGTACAGCAATCTGAACCGATGACAATTAGATCA
TCAAGTCTTGAACGAAATCAACAAGTTCCATTTAATTTTAAAGCAACTTATTCGAGTAGT
TTTGAGAAATTTCAGAATCCACCTCCACCATATATAAAATCAATGAAACCCGTGAAAGGA
GGAAGTTTAGAGCGATCTCAGGCAATTATTATGAATGATTTAATGCGAAAATATTACGAT
CAAAAAGCAGTTGCTGAAGCACAAAAACCAAGAAGTGGTGGAAGTCTTGAGAGAAATTCC
CAGTATCAACAATTTTTATTCATTCAGAAACAACAGCTTCAGCAACAATTGCAAGTTCAA
CAACAGCAAGTTCAAGCACAAAAACAAGCGCAATTACAACAACAACAGCAGCAACAAATG
CAAGAAGATCTCATTGAGGAAAATATTTATGATTTTGGAGGTGTACATGTTAAATCTTGT
GCTACAATTGCACTTAAAAAGAGCATTGAACGTGGAATGTTGCCACCAACAGCTTTAAGA
ACATTTGAATCACCTCAAAATTCAAATCCACCTTCGGGTCCTTCGTCACTCGAAATGAAC
CGTCCAGTAACGCCGCAAGCGGCATTTAAACAACCATGTCCAAGTATTGCAAGTCGAATG
ATGATTTTTCAACAGGGCACAAGTCAACCTGTTCGACCACCAATGCTTCAAAATTCTCCT
ATCCAAAAACCTCCTTTTCCTCATAATCCTAATTTTTTTATTCCACCTATGCAGCCGGAA
ACTATTCAGCATCATCCAAATCAAGATCTACATAACTTTATTGAAGCTCGATTACGAAAG
CAACAGCAAGAAGAAAGTGAAAAAGATGCAAAGTGGTTAAAACAACAAGAAGAAAATATC
AAGAAACGATTAAGCGTATCATCAGTCAATGAATTACCCACTGATGGTCAGAATAGTCAA
AATAGTACTGCAGCTGCAATGCAACCAATGATAGAAACAACTCAACATAGTCCTAAAGCA
GTAAATAAATCACCCTCGTCATCTGCAGTGACATCACCACAAGAATCAATGAGACAAGTT
GAGCCAAAAATAATTGATCGACAGAACGATCCAATTTATAAATGCACCACAAATGTTGTG
AGAGCTGTCATGACATTAAGTAGTGGTGTTGAAAAATCAAATATGAGTGAATATCTCGAT
CTTGTAAAAAATGTTGGACTTGAATTAAGAAATTTATTGGGAACTGTTGATCATATTTCT
TCACAATTTCCACCTCAAACACACAAAGAAGTGGAGATGGCACATAAAGTTTTATCAAAA
GACATGAAAGATCTCGTAGCATCAATGCATAGAGCTATGCAATATTGTGACACAACACTT
GATGTTGAATGTCGAAAAAACATGCTCTCAGCAGCTCATATCCTCGCAATGGACACTAAA
AATCTTCTCGATGTTTGTGATTCAATTCGAATAAGATATCCTAATATCACTTACGAGCTA
CCTGAGAAAACTTTCTCACCTAGTGTCGATCAATGTGTTCTTCTACCTCAAGTTCAACAA
TCACCCAAGAAAAAACCACTTCCGCCGCAGCAAGAATTTTATGAAAATTTAGCTCAGAAT
GTTGAACGATTAGAAATGACTGAGCAATTATATTGTAATCAAAATTTACCGCATACTGAA
ATAGGCATCTATGATAACAGCAGCATCATACAACAAGAACAGTTAAGAATAGTAGAAGAA
CCAACAATGTCACCAACAAATGGCACAAGTAATGGTGTTGAAGCGCAATGA

>g5835.t1 Gene=g5835 Length=1596
MDELSVNSRHFSPNFSPSRNLVGNNSENQTQKSLYIHLVNHGFRMVRVDDSNSDVRQIIS
NVVGSMTSPVGVKPCTQFYALRLRHIVSKEILWLPLSTPTRQVIDYISNESCSNINCPNY
VRSSSPSASSLCDKSQQQQESKENVPLGHSNCVWKIELRVRYIPKSLSEFLERDKITINF
YFNQVKDDFVQSNIASIEQDLAVQLCCLAIRHYYKDARSSNDRKHHLDYIEKEMGFSNFL
PKSVIDTIKLKNLKKLVQSQYKKIYQLSDTDYILKYFELLSTVFDFDHEKFVVTLGQWNI
AIDLIIGYNLGISYLTHSQAKPTKVTDFENILSLKTSILPNTLQQSSISSGSTSGKGLHN
SKSNDSNISQVSSLCGCNNIKSQLRIQVDGNSEDLAITCNGVNTADGIAELIDGYCKIFN
DNNVSLWDKSKTPINSNSLEKRMPAYVQNNDNGGDENEMNLRRVMLSEDYSELHGGVLPE
VEEEGDYSTPTARNYELQRNQIQLNEIIGIGQFGDVYVGTCQIIRSASKKDPTTVREDIV
PVAVKTCKADADLKTSEKFLEEAYVMQKFEHPHIIRLIGICSDPPIWLVMELARLGELRA
YLKENSSKLKLGTLLLYSYQLSTALSYLESKKFVHRDIAARNVLVSSPTCIKLADFGLSR
WVEDQSYYTSSKGLLPIKWMAPESINFRRFTTASDVWMFAVCTWEILMYGVKPFQGIKNS
EVIGKLENGERLALPPNCPPRLYSLMSQCWSYEPAKRPDFKTIKEIMKEILIEEKISDSE
TMKRENRRIAAMSWGAGDEDAPPKPARPMTDSTSKLFTIEDRNENGTSNNSGPQMTYIIA
QNPAVLAQLMRENEKRGLNPSAYTTPASVFNVLAVDFAEDAAATENNAIDQVQLKAMQVP
AMELIPLQQDNTNEILEPSPSLNQIPNFEALGTNVDMSVAYPITSPSGLPPQAPIDNSKT
RSLERNAGQNVPPSVSARVSSLERRQQIQENLKGNQQRSQSLIRQYSAGVQQSEPMTIRS
SSLERNQQVPFNFKATYSSSFEKFQNPPPPYIKSMKPVKGGSLERSQAIIMNDLMRKYYD
QKAVAEAQKPRSGGSLERNSQYQQFLFIQKQQLQQQLQVQQQQVQAQKQAQLQQQQQQQM
QEDLIEENIYDFGGVHVKSCATIALKKSIERGMLPPTALRTFESPQNSNPPSGPSSLEMN
RPVTPQAAFKQPCPSIASRMMIFQQGTSQPVRPPMLQNSPIQKPPFPHNPNFFIPPMQPE
TIQHHPNQDLHNFIEARLRKQQQEESEKDAKWLKQQEENIKKRLSVSSVNELPTDGQNSQ
NSTAAAMQPMIETTQHSPKAVNKSPSSSAVTSPQESMRQVEPKIIDRQNDPIYKCTTNVV
RAVMTLSSGVEKSNMSEYLDLVKNVGLELRNLLGTVDHISSQFPPQTHKEVEMAHKVLSK
DMKDLVASMHRAMQYCDTTLDVECRKNMLSAAHILAMDTKNLLDVCDSIRIRYPNITYEL
PEKTFSPSVDQCVLLPQVQQSPKKKPLPPQQEFYENLAQNVERLEMTEQLYCNQNLPHTE
IGIYDNSSIIQQEQLRIVEEPTMSPTNGTSNGVEAQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
23 g5835.t1 CDD cd14473 FERM_B-lobe 177 282 9.32953E-18
22 g5835.t1 Coils Coil Coil 1110 1130 -
16 g5835.t1 Gene3D G3DSA:3.10.20.90 - 21 111 4.3E-7
21 g5835.t1 Gene3D G3DSA:1.20.80.10 - 162 285 2.8E-39
19 g5835.t1 Gene3D G3DSA:2.30.29.30 - 286 463 7.3E-32
18 g5835.t1 Gene3D G3DSA:3.30.200.20 Phosphorylase Kinase; domain 1 491 592 4.4E-30
20 g5835.t1 Gene3D G3DSA:1.10.510.10 Transferase(Phosphotransferase) domain 1 594 798 2.5E-54
17 g5835.t1 Gene3D G3DSA:1.20.120.330 Nucleotidyltransferases domain 2 1364 1518 3.6E-58
27 g5835.t1 MobiDBLite mobidb-lite consensus disorder prediction 345 365 -
30 g5835.t1 MobiDBLite mobidb-lite consensus disorder prediction 1178 1198 -
31 g5835.t1 MobiDBLite mobidb-lite consensus disorder prediction 1180 1198 -
28 g5835.t1 MobiDBLite mobidb-lite consensus disorder prediction 1304 1359 -
29 g5835.t1 MobiDBLite mobidb-lite consensus disorder prediction 1304 1358 -
4 g5835.t1 PANTHER PTHR46221:SF5 PROTEIN TYROSINE KINASE 2AA 29 1496 1.1E-253
5 g5835.t1 PANTHER PTHR46221 FERM AND PDZ DOMAIN-CONTAINING PROTEIN FAMILY MEMBER 29 1496 1.1E-253
10 g5835.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 590 603 7.0E-29
9 g5835.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 627 645 7.0E-29
8 g5835.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 675 685 7.0E-29
7 g5835.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 694 716 7.0E-29
6 g5835.t1 PRINTS PR00109 Tyrosine kinase catalytic domain signature 738 760 7.0E-29
2 g5835.t1 Pfam PF00373 FERM central domain 173 287 2.8E-6
3 g5835.t1 Pfam PF07714 Protein tyrosine and serine/threonine kinase 502 765 2.6E-87
1 g5835.t1 Pfam PF03623 Focal adhesion targeting region 1365 1493 5.0E-52
26 g5835.t1 ProSitePatterns PS00109 Tyrosine protein kinases specific active-site signature. 633 645 -
32 g5835.t1 ProSiteProfiles PS50057 FERM domain profile. 32 423 31.756
33 g5835.t1 ProSiteProfiles PS50011 Protein kinase domain profile. 502 771 36.513
25 g5835.t1 SMART SM00295 B41_5 28 291 1.6E-15
24 g5835.t1 SMART SM00219 tyrkin_6 502 767 4.5E-122
12 g5835.t1 SUPERFAMILY SSF54236 Ubiquitin-like 31 164 4.13E-12
14 g5835.t1 SUPERFAMILY SSF47031 Second domain of FERM 165 285 1.7E-32
11 g5835.t1 SUPERFAMILY SSF50729 PH domain-like 287 427 7.87E-19
13 g5835.t1 SUPERFAMILY SSF56112 Protein kinase-like (PK-like) 489 776 1.62E-74
15 g5835.t1 SUPERFAMILY SSF68993 FAT domain of focal adhesion kinase 1365 1496 6.67E-47

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5835/g5835.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5835.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005856 cytoskeleton CC
GO:0004713 protein tyrosine kinase activity MF
GO:0005925 focal adhesion CC
GO:0005524 ATP binding MF
GO:0004672 protein kinase activity MF
GO:0006468 protein phosphorylation BP
GO:0007172 signal complex assembly 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