Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein expanded.

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 g4578 g4578.t1 isoform g4578.t1 3286712 3295819
chr_2 g4578 g4578.t1 exon g4578.t1.exon1 3286712 3287304
chr_2 g4578 g4578.t1 cds g4578.t1.CDS1 3286712 3287304
chr_2 g4578 g4578.t1 exon g4578.t1.exon2 3287366 3290480
chr_2 g4578 g4578.t1 cds g4578.t1.CDS2 3287366 3290480
chr_2 g4578 g4578.t1 exon g4578.t1.exon3 3290549 3290628
chr_2 g4578 g4578.t1 cds g4578.t1.CDS3 3290549 3290628
chr_2 g4578 g4578.t1 exon g4578.t1.exon4 3295499 3295644
chr_2 g4578 g4578.t1 cds g4578.t1.CDS4 3295499 3295644
chr_2 g4578 g4578.t1 exon g4578.t1.exon5 3295710 3295819
chr_2 g4578 g4578.t1 cds g4578.t1.CDS5 3295710 3295819
chr_2 g4578 g4578.t1 TSS g4578.t1 NA NA
chr_2 g4578 g4578.t1 TTS g4578.t1 NA NA

Sequences

>g4578.t1 Gene=g4578 Length=4044
ATGCGAGCTTTTTGTACCGTCAGCGCACCCCTAGAGGTTTGCGCTCCACCATCAAGACCG
CCATTACCATTACCTCCGCTTCCAGCAAATGCACGCTTTCTGGCTTTGAAACTATTCGGA
ACGCCACAATCACGCACTCTCTACTTCCTAGTCGAAGCAAAAAGTCGTGTACGAGAAGTT
TACGCACAAACATGTCATCATTTCTCAAAGCAAGGAATGCTGGACACCGAACTGTTCGGT
TTGGCAGTTCTCATAGATGGGGAGTATCTATTTGCAGATCCCGAGTCCAAACTATCAAAA
TACGGCCCAAAAAGTTGGCGATCATCGCACACTCATGGCCTTGATGCAAATGGCAAACCT
CTCTTAGAATTTCACTTCCGCGTACAATTTTATATTGAAAGTCCACTTATGTTAAGAGAT
GAAATTACGCGGCATCATTATTATTTACAACTCAAAACAAATGCAGTGGGTCGCGAAATT
CCAAAGGACTGTTCTGACCAATCACTGCTTCTACTTGGAGGTCTAGCACTTCAGGCTGAT
TTGGGCGATTGTCCCGATGATCAATCGACAACAGCTGCTGGATCTTCATCCACAGCAACC
TCATCAACAGATTATTTTCGAGCTGATGACTATATTCCATCAACACTACGTACCACGTGG
GGCATTTCAGCATTACATTCTTGCCATAGAGAAAATCGTGGAATGTCACGTGCAGATGCA
GAAACGCACTTCATACGCGAAGCATGTGGACTTCATGAGGCCATAAACGCTCACATTTTT
AGAATGAAAAGCAACAAAAGTGAAAACGGTGTTGGTTCAGTAATGTTAATTATATACGCT
AAAGGTCTAAAAATAGTTAATGAAACGTCACCACCTGTCACCTTTCTTTGGCCCTCAATT
AGCAAATTAAGTTTTGATCGTAAAAAGTTTGAACTGCGTTCGGGTGAAAATAAAATCACT
CTGTACTCAAGCAATGATGATAAAAACAAGATGCTGCTAGCACTTTGTCGAGAGACTCAT
CAATTTTCCATGAAAATTGCTCCACGTCTAACGGAAGCGATGAAACGAGAGGAGGAGGAA
AGTAATTGCATACACGCATGCTATCTATACTCGCGTGCACTTAACATGCAATATAAGAGT
AAAAACGATCAGAGAATTTCGGTCATATCGAGCACGAGCAGTAATACGACGTCGGGAATT
GTCAGCGATCGCGTGCATTCTGAAGATGAGCTAGAAATTCTTATCAATACTCCTCCTATA
GCGGCGCCATCCACAGAGAGTCTTGCACTCGCTCATTTGCTTGACTGCCCAAGTGTCTCA
CGTCAGACATCTTCAGTTGGTCAAGTTTCGCTCAAAGATATTGGCGACACATTTGCAGCA
CTTTCCATTCGATCAAATACTCGTTCAACAAGCAGTGAAGGAACAGAAACATTAAAAGAA
AAAACAAGCGAGAAAGATTGCGATGTATCGCCATCATCACAACACAATGTTGGTTCACAA
TGTTCATCAACATGCAGCACAGTTGTTGTTGTTAATTCACAGCAGTCACAATTCAATGGA
AGCAATCGTAGCAGTGAACGTAGACAATCTTCAACTTGCAGTAGCTTAGAATTAGGATTT
AGTCATACAGCTCAAAATTCAGCAGTCAGTGAGAGCACAAATAATGATAATCATCACTAT
GGCACAACAGATACACAAAATGATGATGAAGAAACAATTTCTGGAGTTTATGCACTTGAT
AATAATGCACCAACTGAAACAAGCGGAGTTTATACGATGAATAGCAGTGAAATGACTGGA
GAATCTTCAGAAATTGCTGAATCAGAGTCACATGAAAGTTCACATTATGGAAGTTTTCAT
CCAAATAGTGAAATGGGTGACAAACTTGTTGTCAACATAAACATCGATTCAGTTGATGGT
GATTTTCGGCAGAGATTAGATAGTGAAGTTGGTCGATTTAGAATGCGATCAGATTCAAAT
ATTAGTGCTGCTGGCTCATTTAGAGGCGATGGTAGTGATCCAACTGATAAGAAACATAAT
CCTTTAACTGCGGAAGAACTTACAGATTTGATTGTTGGTCGAGGAACTTATCCATCACGT
AAAACAGTCAGCGATACAATGGATTCAGATTGTGATTATGTCACATTGCCTATTCCATTA
GAAGGTGAAAGTTATTTGCAAGGAAGTGAAGATACTGCACCAACTGAAGATGAATATGAG
AAAGATTTATTAGAAGTCACCCCACCAGCACCACCTCAAAGAATTGATAGCATGTCATTG
TCAAATATTGTTGAAATGCCTCAACCACCGCCATATAATTCTCATCATGAAACAACTGGT
TTAAGAGGTCCTGATATTTCAAGTCCTGAACTTGCTTCAATTCCATTGCGTGATTCTCAA
ATTTATCCAAGAAAGTCATTGAGATCACTTTCTACAATCATTCCTCCAACAACAATTCCA
GAAGAAACTCCAGCACGTTTCATCACAACTCGTCCACATATTAATATACTTAAGGCTCAT
ACTACTTTAGTTGGAGAGAAACCAAGTTATGCAGCACCAACAGTCAATACTATCAACAAT
TTATCTCAATCGCCACTTCCTACAGCTACATCACTAGGTATTCCATATGTTCCCTACCAT
AATTTGCATGCAACGCACAAAACTCACTTGTCGCACTCACAATCAGCTTCTGCACCAAGA
ACTTGTGTATTGCTGCCAGTTATCAAACCACGCACGCAATCTTATGTTCCACCACCTATG
CAAACACATCGACAACCACCGCCACCACCTCCAACACAACCTCAATTAGCTACAGTCTAC
ACAAGCCAGCTTGCACGATCACAAATTGAACTTTATCAACAGCAATTATATAGTGATGTC
GATTATGTAATTTATCCATTACAAGATCCAGCTGTGAGTCAGCAAGAATATCTTGATTCA
AAACAAGGCTCAATTTTGGCGGCAATGGCACAAACACAACCGCCACCATATCTAGCATAT
CATACTGTTCGTGCACATAACAGAAGTTGGGATGGCAATCCTGCTATTTATCGTAGCACT
CCTTTCCTTTCGATGGCAATTTCATCACCATCACGTTACGCTTCAACACAGAATTTGTCT
GATACTTATGTACAATTGCCAGGCACATATTCACCACTTTACTCACCGTCTGTAGCAAGT
TTATGCTCATCATATGAACCACCGCCACCTTTACCGCCACTTAGACCACCGAGAATTACA
CAGAAAGCTACAAGCACACTCTCAACACCAACTAAACTATTTTCACGATCGAGATCAGAT
GATAATATTTTAAATTCGATAGATGATACACCACAATCAAAACGACGACCAATTCCAATA
CCACCGGCATATGAGAAGAAACCAATTAGGAAACCACCTATGCCTGCGCCCATTGAGAGC
TGTTTGGAACTTGCATCAACTCCACCATCAGTGCCTGCTAAACCATCAACATTGAAGACT
TCCTCCTCTTCATCAAGTATGAAATTGCAGTCAAAGTCTTCAACAAATCTCACAACCTGC
GTAGACACTCCAAAAATGGCAACATCAACAAGTCAGTCAACAACAACACCTGCAAAACCA
TTTGATTTGAAACTCTCACATGTCATTTGTCCCGAATCAAATCGAATAATTGCACCAGTC
AGTCTTCAACAGCAACTTGATATTAGCATCTTGCGTGAGAAAAGTCGAAATCTCGATTTG
CCATTAATTTCGGCTCTCTGCAATGATCGTTCCTTATTGAAGCAGACAAAAGCATTTGTG
CAACCAAAACAGCAACGTTCATCGCTTCAAAATAACAGCAGCTCAACTCTCTCATCCAAG
TCGAAATATCCTGTATCAGGACTTAGCACAACACAGCTCTCATCGACTACAAAGAGTCGT
AAGACTACAATAAGTCATCGACATCCACAAGATAAATTGCCACCTTTACCTGTAAGCAAC
AATAATAGTGCTGTAAAGAATAATTATGTAATGGATCCAATACCACTGAAACAAAAAACA
AATCAGCAAAATACAAATCTATAG

>g4578.t1 Gene=g4578 Length=1347
MRAFCTVSAPLEVCAPPSRPPLPLPPLPANARFLALKLFGTPQSRTLYFLVEAKSRVREV
YAQTCHHFSKQGMLDTELFGLAVLIDGEYLFADPESKLSKYGPKSWRSSHTHGLDANGKP
LLEFHFRVQFYIESPLMLRDEITRHHYYLQLKTNAVGREIPKDCSDQSLLLLGGLALQAD
LGDCPDDQSTTAAGSSSTATSSTDYFRADDYIPSTLRTTWGISALHSCHRENRGMSRADA
ETHFIREACGLHEAINAHIFRMKSNKSENGVGSVMLIIYAKGLKIVNETSPPVTFLWPSI
SKLSFDRKKFELRSGENKITLYSSNDDKNKMLLALCRETHQFSMKIAPRLTEAMKREEEE
SNCIHACYLYSRALNMQYKSKNDQRISVISSTSSNTTSGIVSDRVHSEDELEILINTPPI
AAPSTESLALAHLLDCPSVSRQTSSVGQVSLKDIGDTFAALSIRSNTRSTSSEGTETLKE
KTSEKDCDVSPSSQHNVGSQCSSTCSTVVVVNSQQSQFNGSNRSSERRQSSTCSSLELGF
SHTAQNSAVSESTNNDNHHYGTTDTQNDDEETISGVYALDNNAPTETSGVYTMNSSEMTG
ESSEIAESESHESSHYGSFHPNSEMGDKLVVNINIDSVDGDFRQRLDSEVGRFRMRSDSN
ISAAGSFRGDGSDPTDKKHNPLTAEELTDLIVGRGTYPSRKTVSDTMDSDCDYVTLPIPL
EGESYLQGSEDTAPTEDEYEKDLLEVTPPAPPQRIDSMSLSNIVEMPQPPPYNSHHETTG
LRGPDISSPELASIPLRDSQIYPRKSLRSLSTIIPPTTIPEETPARFITTRPHINILKAH
TTLVGEKPSYAAPTVNTINNLSQSPLPTATSLGIPYVPYHNLHATHKTHLSHSQSASAPR
TCVLLPVIKPRTQSYVPPPMQTHRQPPPPPPTQPQLATVYTSQLARSQIELYQQQLYSDV
DYVIYPLQDPAVSQQEYLDSKQGSILAAMAQTQPPPYLAYHTVRAHNRSWDGNPAIYRST
PFLSMAISSPSRYASTQNLSDTYVQLPGTYSPLYSPSVASLCSSYEPPPPLPPLRPPRIT
QKATSTLSTPTKLFSRSRSDDNILNSIDDTPQSKRRPIPIPPAYEKKPIRKPPMPAPIES
CLELASTPPSVPAKPSTLKTSSSSSSMKLQSKSSTNLTTCVDTPKMATSTSQSTTTPAKP
FDLKLSHVICPESNRIIAPVSLQQQLDISILREKSRNLDLPLISALCNDRSLLKQTKAFV
QPKQQRSSLQNNSSSTLSSKSKYPVSGLSTTQLSSTTKSRKTTISHRHPQDKLPPLPVSN
NNSAVKNNYVMDPIPLKQKTNQQNTNL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4578.t1 CDD cd17101 FERM_F1_PTPN13_like 32 134 1.56058E-34
10 g4578.t1 CDD cd14473 FERM_B-lobe 143 251 1.64419E-7
12 g4578.t1 CDD cd13185 FERM_C_FRMD1_FRMD6 253 354 7.99445E-42
9 g4578.t1 Gene3D G3DSA:1.20.80.10 - 129 252 4.5E-22
8 g4578.t1 Gene3D G3DSA:2.30.29.30 - 257 342 1.5E-10
18 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 465 494 -
15 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 474 488 -
23 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 516 535 -
24 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 547 569 -
20 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 595 617 -
19 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1082 1132 -
22 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1082 1112 -
16 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1115 1132 -
26 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1146 1178 -
25 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1150 1178 -
17 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1259 1322 -
21 g4578.t1 MobiDBLite mobidb-lite consensus disorder prediction 1259 1300 -
3 g4578.t1 PANTHER PTHR13429:SF10 PROTEIN EXPANDED 1 1344 0.0
4 g4578.t1 PANTHER PTHR13429 FERM DOMAIN (PROTEIN4.1-EZRIN-RADIXIN-MOESIN) FAMILY 1 1344 0.0
2 g4578.t1 Pfam PF00373 FERM central domain 137 258 1.8E-14
1 g4578.t1 Pfam PF09380 FERM C-terminal PH-like domain 273 348 1.2E-11
27 g4578.t1 ProSiteProfiles PS50057 FERM domain profile. 32 347 48.707
14 g4578.t1 SMART SM00295 B41_5 30 259 1.1E-30
13 g4578.t1 SMART SM01196 FERM_C_3 268 351 1.6E-19
6 g4578.t1 SUPERFAMILY SSF54236 Ubiquitin-like 46 133 1.05E-5
7 g4578.t1 SUPERFAMILY SSF47031 Second domain of FERM 133 251 7.33E-19
5 g4578.t1 SUPERFAMILY SSF50729 PH domain-like 256 386 2.43E-17

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

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