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.t11 TTS g10146.t11 7779582 7779582
chr_1 g10146 g10146.t11 isoform g10146.t11 7780212 7782838
chr_1 g10146 g10146.t11 exon g10146.t11.exon1 7780212 7780429
chr_1 g10146 g10146.t11 cds g10146.t11.CDS1 7780247 7780429
chr_1 g10146 g10146.t11 exon g10146.t11.exon2 7780505 7780748
chr_1 g10146 g10146.t11 cds g10146.t11.CDS2 7780505 7780748
chr_1 g10146 g10146.t11 exon g10146.t11.exon3 7780821 7780944
chr_1 g10146 g10146.t11 cds g10146.t11.CDS3 7780821 7780944
chr_1 g10146 g10146.t11 exon g10146.t11.exon4 7781000 7781330
chr_1 g10146 g10146.t11 cds g10146.t11.CDS4 7781000 7781330
chr_1 g10146 g10146.t11 exon g10146.t11.exon5 7781396 7781918
chr_1 g10146 g10146.t11 cds g10146.t11.CDS5 7781396 7781584
chr_1 g10146 g10146.t11 exon g10146.t11.exon6 7782775 7782838
chr_1 g10146 g10146.t11 TSS g10146.t11 7782841 7782841

Sequences

>g10146.t11 Gene=g10146 Length=1504
AGAAGAAAAAAAAGTTTTCGATCAGAATGTAAAATTTCTGTTTTAGTGTTAAAATGCATT
AAAAGGCATCATAATATAAATGTGACATCTAACGATAGCAAAAAGTGTGTGTAGTTGAAA
AAAAAATTAAAAGAAAGTATTAGCTTACTTATGTATCAAATACATGCATATAAAAAATTG
TTGATTTGATAAAAAAGAGAGTGTTGATATATCAAAGTAAAGAGTTTAAATTTTTTTTTG
AAGTGTTAGGAAAAAAGAAGCAAAGCATGAACGTTCTATAGTGAATATATATATTTTAGA
GTGACTGTTACTAATTCAATTTGGTGATTTTCAAAAAATCTTTTTAAAAGCAAAATTTAA
ATAAAAATTTAAGGTGAAGAAAAGAGAAAATTATTATAATGTCATTAAATTCATTGGGCA
CATCAAATACAAATGGACTGCCAAGCAGTCGCATGACACATTCGTTGAGTACACCATCAG
GGGTCGATGGATCGTCTGCTGTCACGCAACATTCGCGAGGTGGTGGAAAAAAGCTCGCAA
TTCGTGTACAAATGTTGGATGATTCAATGACACTCTTTCAAGTTCAGGCAAAGGCACTTG
GAAAAGTTTTATTTGAGCAAGTCTGTCGACAATTGAATCTTCTTGAAGCAGATTATTTTG
GACTTGAATATACAGAAAGTTCGTCAGGCACAAAATATTGGTTGGATTTAGAAAAACCAC
TCAATAGACAAGTTGGTTTCTCGCTCATTGATCCACTTTTGAGATTTTGCGTGAAATTTT
ATGCCAATGATCCAACACAACTCGAAGAAGAGTATACGAGGTATTTGTTTTGTCTACAAA
TCAAGAGGGATTTGGCTACGGGCAGTTTGCAATGTAACGACAATACAGCAGCTTTAATGG
CCAGTTATATCGTGCAAGCCTCTTGTGGTGATTATTCCTTTGAGGACTATCCCGATCACA
CTTATCTATCTTCGTATCGATTTGTACCACAGCAAGATCAAACGCTTCAGCGAAAAATAA
TGGAAAATCATAAAAAGCATATTGGACAATCGCCAGCTGAAGCAGACTTAAATCTTTTGG
AGACTGCAAGACGTTGTGAACTTTATGGCATGAAAATGCATGCAGCCAAAGACCATGAGG
GTGTTCCATTGAACTTATCTGTCGCGCACTTTGGCATTGCTGTTTTTCAGGGCATCACGC
GCATCAATACATTTTCATGGGCTAAAATTCGTAAACTTTCGTTTAAACGTAAAAAGTTTT
TAATAAAACTTCATCCAGAGGGATATGGCTATTACAAAGACATTGTCGAATTTTTCTTTG
AAGGCAGAAATGAATGTAAAAATTTTTGGAAAAAATGTGTTGAAAATCATGGCTTTTTCC
GATGTCAAGCAGTTCAGAGTGCTCCAAGAAGGAAAACAAGAGTAAGTGCTGACATTTTAT
ATAAAGCTTATCAAATTGTGTCTTATTAACTCAATATGATATATTTTCCACATGCGCGGT
TACA

>g10146.t11 Gene=g10146 Length=356
MSLNSLGTSNTNGLPSSRMTHSLSTPSGVDGSSAVTQHSRGGGKKLAIRVQMLDDSMTLF
QVQAKALGKVLFEQVCRQLNLLEADYFGLEYTESSSGTKYWLDLEKPLNRQVGFSLIDPL
LRFCVKFYANDPTQLEEEYTRYLFCLQIKRDLATGSLQCNDNTAALMASYIVQASCGDYS
FEDYPDHTYLSSYRFVPQQDQTLQRKIMENHKKHIGQSPAEADLNLLETARRCELYGMKM
HAAKDHEGVPLNLSVAHFGIAVFQGITRINTFSWAKIRKLSFKRKKFLIKLHPEGYGYYK
DIVEFFFEGRNECKNFWKKCVENHGFFRCQAVQSAPRRKTRVSADILYKAYQIVSY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
21 g10146.t11 CDD cd17098 FERM_F1_FARP1_like 46 132 7.84308E-43
19 g10146.t11 CDD cd14473 FERM_B-lobe 140 233 4.04761E-26
20 g10146.t11 CDD cd13193 FERM_C_FARP1-like 228 345 4.94883E-81
16 g10146.t11 Gene3D G3DSA:3.10.20.90 - 44 126 4.1E-23
18 g10146.t11 Gene3D G3DSA:1.20.80.10 - 127 235 1.1E-36
17 g10146.t11 Gene3D G3DSA:2.30.29.30 - 236 328 1.0E-34
25 g10146.t11 MobiDBLite mobidb-lite consensus disorder prediction 1 39 -
26 g10146.t11 MobiDBLite mobidb-lite consensus disorder prediction 1 40 -
4 g10146.t11 PANTHER PTHR45858 FERM DOMAIN CONTAINING PROTEIN 7 342 1.3E-216
5 g10146.t11 PANTHER PTHR45858:SF5 CHONDROCYTE-DERIVED EZRIN-LIKE DOMAIN CONTAINING PROTEIN, ISOFORM G 7 342 1.3E-216
12 g10146.t11 PRINTS PR00661 ERM family signature 59 78 1.4E-7
8 g10146.t11 PRINTS PR00935 Band 4.1 protein family signature 79 91 7.5E-19
6 g10146.t11 PRINTS PR00935 Band 4.1 protein family signature 146 159 7.5E-19
10 g10146.t11 PRINTS PR00661 ERM family signature 155 176 1.4E-7
7 g10146.t11 PRINTS PR00935 Band 4.1 protein family signature 159 179 7.5E-19
9 g10146.t11 PRINTS PR00935 Band 4.1 protein family signature 221 237 7.5E-19
11 g10146.t11 PRINTS PR00661 ERM family signature 244 264 1.4E-7
3 g10146.t11 Pfam PF09379 FERM N-terminal domain 50 112 7.9E-20
2 g10146.t11 Pfam PF00373 FERM central domain 132 241 3.3E-16
1 g10146.t11 Pfam PF09380 FERM C-terminal PH-like domain 245 331 1.9E-22
24 g10146.t11 ProSitePatterns PS00660 FERM domain signature 1. 101 131 -
27 g10146.t11 ProSiteProfiles PS50057 FERM domain profile. 46 331 76.596
23 g10146.t11 SMART SM00295 B41_5 42 241 2.3E-57
22 g10146.t11 SMART SM01196 FERM_C_3 245 335 3.0E-33
14 g10146.t11 SUPERFAMILY SSF54236 Ubiquitin-like 48 129 2.21E-21
15 g10146.t11 SUPERFAMILY SSF47031 Second domain of FERM 131 236 1.44E-31
13 g10146.t11 SUPERFAMILY SSF50729 PH domain-like 234 336 1.32E-31

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

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