Gene loci information

Transcript annotation

  • This transcript has been annotated as FERM, ARHGEF and pleckstrin domain-containing protein 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_1 g10146 g10146.t9 isoform g10146.t9 7778997 7782838
chr_1 g10146 g10146.t9 exon g10146.t9.exon1 7778997 7778998
chr_1 g10146 g10146.t9 cds g10146.t9.CDS1 7778997 7778998
chr_1 g10146 g10146.t9 exon g10146.t9.exon2 7779171 7779274
chr_1 g10146 g10146.t9 cds g10146.t9.CDS2 7779171 7779274
chr_1 g10146 g10146.t9 exon g10146.t9.exon3 7780018 7780092
chr_1 g10146 g10146.t9 cds g10146.t9.CDS3 7780018 7780092
chr_1 g10146 g10146.t9 exon g10146.t9.exon4 7780185 7780210
chr_1 g10146 g10146.t9 cds g10146.t9.CDS4 7780185 7780210
chr_1 g10146 g10146.t9 exon g10146.t9.exon5 7780295 7780429
chr_1 g10146 g10146.t9 cds g10146.t9.CDS5 7780295 7780429
chr_1 g10146 g10146.t9 exon g10146.t9.exon6 7780505 7780748
chr_1 g10146 g10146.t9 cds g10146.t9.CDS6 7780505 7780748
chr_1 g10146 g10146.t9 exon g10146.t9.exon7 7780821 7780944
chr_1 g10146 g10146.t9 cds g10146.t9.CDS7 7780821 7780944
chr_1 g10146 g10146.t9 exon g10146.t9.exon8 7781000 7781330
chr_1 g10146 g10146.t9 cds g10146.t9.CDS8 7781000 7781330
chr_1 g10146 g10146.t9 exon g10146.t9.exon9 7781396 7781918
chr_1 g10146 g10146.t9 cds g10146.t9.CDS9 7781396 7781584
chr_1 g10146 g10146.t9 exon g10146.t9.exon10 7782775 7782838
chr_1 g10146 g10146.t9 TSS g10146.t9 7782841 7782841
chr_1 g10146 g10146.t9 TTS g10146.t9 NA NA

Sequences

>g10146.t9 Gene=g10146 Length=1628
AGAAGAAAAAAAAGTTTTCGATCAGAATGTAAAATTTCTGTTTTAGTGTTAAAATGCATT
AAAAGGCATCATAATATAAATGTGACATCTAACGATAGCAAAAAGTGTGTGTAGTTGAAA
AAAAAATTAAAAGAAAGTATTAGCTTACTTATGTATCAAATACATGCATATAAAAAATTG
TTGATTTGATAAAAAAGAGAGTGTTGATATATCAAAGTAAAGAGTTTAAATTTTTTTTTG
AAGTGTTAGGAAAAAAGAAGCAAAGCATGAACGTTCTATAGTGAATATATATATTTTAGA
GTGACTGTTACTAATTCAATTTGGTGATTTTCAAAAAATCTTTTTAAAAGCAAAATTTAA
ATAAAAATTTAAGGTGAAGAAAAGAGAAAATTATTATAATGTCATTAAATTCATTGGGCA
CATCAAATACAAATGGACTGCCAAGCAGTCGCATGACACATTCGTTGAGTACACCATCAG
GGGTCGATGGATCGTCTGCTGTCACGCAACATTCGCGAGGTGGTGGAAAAAAGCTCGCAA
TTCGTGTACAAATGTTGGATGATTCAATGACACTCTTTCAAGTTCAGGCAAAGGCACTTG
GAAAAGTTTTATTTGAGCAAGTCTGTCGACAATTGAATCTTCTTGAAGCAGATTATTTTG
GACTTGAATATACAGAAAGTTCGTCAGGCACAAAATATTGGTTGGATTTAGAAAAACCAC
TCAATAGACAAGTTGGTTTCTCGCTCATTGATCCACTTTTGAGATTTTGCGTGAAATTTT
ATGCCAATGATCCAACACAACTCGAAGAAGAGTATACGAGGTATTTGTTTTGTCTACAAA
TCAAGAGGGATTTGGCTACGGGCAGTTTGCAATGTAACGACAATACAGCAGCTTTAATGG
CCAGTTATATCGTGCAAGCCTCTTGTGGTGATTATTCCTTTGAGGACTATCCCGATCACA
CTTATCTATCTTCGTATCGATTTGTACCACAGCAAGATCAAACGCTTCAGCGAAAAATAA
TGGAAAATCATAAAAAGCATATTGGACAATCGCCAGCTGAAGCAGACTTAAATCTTTTGG
AGACTGCAAGACGTTGTGAACTTTATGGCATGAAAATGCATGCAGCCAAAGACCATGAGG
GTGTTCCATTGAACTTATCTGTCGCGCACTTTGGCATTGCTGTTTTTCAGGGCATCACGC
GCATCAATACATTTTCATGGGCTAAAATTCGTAAACTTTCGTTTAAACGTAAAAAGTTTT
TAATAAAACTTCATCCAGAGGGATATGGCTATTACAAAGACATTGTCGAATTTTTCTTTG
AAGGCAGAAATGAATGTAAAAATTTTTGGAAAAAATGTGTTGAAAATCATGGCTTTTTCC
GATGTCAAGCAGTTCAGAGTGCTCCAAGAAGGAAAACAAGAGTTCTCTCTCGAGGAAGTT
CATTTCGTTATAGTGGAAAGACTCAAAAACAAATTATCGAGTTTGTACGTGAAAATTATG
TAAAACGACAAACGTTCCAAAGGTCTCAATCGTTTCGTCAGGGCCCGTTAGCAAGTAAAA
GAAGTCAATCGCAAAATGTTGTTAATACAAGCATCTCAGCACATCCTTTACTTCCCATTG
AGACCGCG

>g10146.t9 Gene=g10146 Length=410
MSLNSLGTSNTNGLPSSRMTHSLSTPSGVDGSSAVTQHSRGGGKKLAIRVQMLDDSMTLF
QVQAKALGKVLFEQVCRQLNLLEADYFGLEYTESSSGTKYWLDLEKPLNRQVGFSLIDPL
LRFCVKFYANDPTQLEEEYTRYLFCLQIKRDLATGSLQCNDNTAALMASYIVQASCGDYS
FEDYPDHTYLSSYRFVPQQDQTLQRKIMENHKKHIGQSPAEADLNLLETARRCELYGMKM
HAAKDHEGVPLNLSVAHFGIAVFQGITRINTFSWAKIRKLSFKRKKFLIKLHPEGYGYYK
DIVEFFFEGRNECKNFWKKCVENHGFFRCQAVQSAPRRKTRVLSRGSSFRYSGKTQKQII
EFVRENYVKRQTFQRSQSFRQGPLASKRSQSQNVVNTSISAHPLLPIETA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
22 g10146.t9 CDD cd17098 FERM_F1_FARP1_like 46 132 1.35709E-42
20 g10146.t9 CDD cd14473 FERM_B-lobe 140 233 3.93156E-26
21 g10146.t9 CDD cd13193 FERM_C_FARP1-like 228 349 5.34452E-84
17 g10146.t9 Gene3D G3DSA:3.10.20.90 - 44 126 5.2E-23
19 g10146.t9 Gene3D G3DSA:1.20.80.10 - 127 235 1.5E-36
18 g10146.t9 Gene3D G3DSA:2.30.29.30 - 236 328 1.3E-34
27 g10146.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 39 -
28 g10146.t9 MobiDBLite mobidb-lite consensus disorder prediction 1 40 -
5 g10146.t9 PANTHER PTHR45858 FERM DOMAIN CONTAINING PROTEIN 7 393 4.0E-244
6 g10146.t9 PANTHER PTHR45858:SF5 CHONDROCYTE-DERIVED EZRIN-LIKE DOMAIN CONTAINING PROTEIN, ISOFORM G 7 393 4.0E-244
13 g10146.t9 PRINTS PR00661 ERM family signature 59 78 2.0E-7
9 g10146.t9 PRINTS PR00935 Band 4.1 protein family signature 79 91 1.2E-18
7 g10146.t9 PRINTS PR00935 Band 4.1 protein family signature 146 159 1.2E-18
11 g10146.t9 PRINTS PR00661 ERM family signature 155 176 2.0E-7
8 g10146.t9 PRINTS PR00935 Band 4.1 protein family signature 159 179 1.2E-18
10 g10146.t9 PRINTS PR00935 Band 4.1 protein family signature 221 237 1.2E-18
12 g10146.t9 PRINTS PR00661 ERM family signature 244 264 2.0E-7
4 g10146.t9 Pfam PF09379 FERM N-terminal domain 50 112 9.8E-20
3 g10146.t9 Pfam PF00373 FERM central domain 132 241 4.3E-16
2 g10146.t9 Pfam PF09380 FERM C-terminal PH-like domain 245 331 2.4E-22
1 g10146.t9 Pfam PF08736 FERM adjacent (FA) 342 381 7.0E-13
26 g10146.t9 ProSitePatterns PS00660 FERM domain signature 1. 101 131 -
29 g10146.t9 ProSiteProfiles PS50057 FERM domain profile. 46 331 76.596
25 g10146.t9 SMART SM00295 B41_5 42 241 2.3E-57
23 g10146.t9 SMART SM01196 FERM_C_3 245 335 3.0E-33
24 g10146.t9 SMART SM01195 FA_2 340 386 3.3E-15
15 g10146.t9 SUPERFAMILY SSF54236 Ubiquitin-like 48 129 2.81E-21
16 g10146.t9 SUPERFAMILY SSF47031 Second domain of FERM 131 236 1.83E-31
14 g10146.t9 SUPERFAMILY SSF50729 PH domain-like 234 379 4.3E-39

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:0005856 cytoskeleton CC
GO:0008092 cytoskeletal protein binding MF

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