Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA repair protein RAD50.

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 g5624 g5624.t1 TTS g5624.t1 10711070 10711070
chr_2 g5624 g5624.t1 isoform g5624.t1 10711128 10715366
chr_2 g5624 g5624.t1 exon g5624.t1.exon1 10711128 10712938
chr_2 g5624 g5624.t1 cds g5624.t1.CDS1 10711128 10712938
chr_2 g5624 g5624.t1 exon g5624.t1.exon2 10713002 10714281
chr_2 g5624 g5624.t1 cds g5624.t1.CDS2 10713002 10714281
chr_2 g5624 g5624.t1 exon g5624.t1.exon3 10714341 10714921
chr_2 g5624 g5624.t1 cds g5624.t1.CDS3 10714341 10714921
chr_2 g5624 g5624.t1 exon g5624.t1.exon4 10714980 10715115
chr_2 g5624 g5624.t1 cds g5624.t1.CDS4 10714980 10715115
chr_2 g5624 g5624.t1 exon g5624.t1.exon5 10715173 10715228
chr_2 g5624 g5624.t1 cds g5624.t1.CDS5 10715173 10715228
chr_2 g5624 g5624.t1 exon g5624.t1.exon6 10715298 10715366
chr_2 g5624 g5624.t1 cds g5624.t1.CDS6 10715298 10715366
chr_2 g5624 g5624.t1 TSS g5624.t1 10715459 10715459

Sequences

>g5624.t1 Gene=g5624 Length=3933
ATGTCACTACTTAATAAACTGCATATACAAGGTATTCGTTCTTTTGGTCTTGATAAAGAA
GATGAACAAAGAATTGAATTTACATCTCCTGTTACATTGATTGTTGGTGAAAACGGTTGT
GGAAAAACAACTATAATTGAGTGCCTGAAATATGCATTGACCGGTGATGTCCCGCCTGGA
TCTGATCGAGGAAAAAATTTTATTCATGAATCTAATCTTCATGCTAATCGTACAATATTT
ATGGGAAAAGTTAAACTTACTGTGACAGATTCACAACAAGTTGATAAGACTGTAGTACGA
GCTATGAAATTAGATAATTCAAAAGCCAAACCAAAATTTGAAACTCTGAATTCTTCAATA
ACCTTTCAACACAAAAATGGTCAACGTGAAGATGTAAGCGGTAGAGTAGATGATATAAAT
AATTATATGTGTGAAACAATGGGTGTTTCGAAATCTATTCTTAACAATGTCATATTTTGT
CATCAAGAAGATTCAAATTGGCCACTCGATGAAGGCAAGAAGCTTAAGGAGAAATTTGAT
GCTATCTTTGGTACAACTGAATACAACAAAGCAATAGATAGAATCATAAAGATTCGTAAA
GAATATCAGAAACAATTAGCTGAAATAAAAGGTGATATCAAGTACAATGCAGAAATAAAG
AGTCAAGTGGATAAAAAGGAAAGGAAAATTAAAGAACTTCAAGCTGAACTTAATGGAGTT
GATGATAAATTTAAGAAACTTGAAGATGCTTTAATCCCACTTCAAGAAGAAAATTTGAAA
ATCTTGGAAAAAGAACGGAACTACAGTAAACATTTATCTGAGCAGCAAAATTGTAGAAAT
ATATTCAATAACAAAAAGGATGAATATGTTAAATTACAAGAAAGAATTACTAAAAATGGC
GGAAAAATCGACAGAGATTTAGAATCTTTGAAACAACAACAATTAAATTTTGAAAAAGAT
CGACAAGATCGAGAGAAAAACAAGGAATCTCTTGAAGAAGAATGCAAAAAGCTCAAATCT
TTAAAGGAGAAGAAGAGAAATGATATGATGACTCTCAATGGAAAGATGCATGAATATACT
AGTGATTATCAGCGTCTTCAAGATATTTTTGCAGAAAGATTTGATAAAATGCAAGAAATA
TGTTCTAAACTTAACATTCCATTTACCGATGATATGGATCAGTCAATAAACACTCAATCT
CTTGCTGATACATTGAGTAATATTAAACAATATATTTTAAGTGCTGAAGAAAATTTTGTA
CGTTTAAAAGCTGAAGCAAAAAAAGATGAAGATGCATATCAGTTAAACATTGATAAAATC
CGTGAAGAACGTACAAAATTGGAAACAAATATAGCAACACAGCGAAATTTAATCCAGGAA
AAAACTGAAATTATTGCAAAACTTAAAAGAGAAATTGCAAGTACTGAAAGTCTCATTCCA
AAGCTCAAGGAAATTCAACCACAGATAGAAGCAACTGAAAAAAAATTAAAACGGCTAAAT
GATGAAAACAATACTGAAGATATGACACTGCAGCAAAGCCTTCTGCAAACTGAAATATTG
GAATTAGAAGATGATCAAGTAAAAATTGACAAAAGTATCGAAGTTTTGCACTCTGCATCA
CAATTTACAAACGAACTCGAATCAAAGCAAAAGGAATTGACTGAGAATCAAAAAGAATAT
ACTCGATTGAAAAACAAATCTGCATCAAATTTTAAAGCTCTTTTCTCAAACAAAGATATT
GAAAACAATTTTCATCATCAAATGCAAGCAAAACAAACGGAGCTTAAAAAAGGAATCAAT
GATGTTGAAACGAAAATTAAAGAAAAGCAACATGAAAAAGATCGTATTATTATGGAACGT
AACAATTTACGTAAAACTGAAGAGAAATTAGAAGACGAAATTAGAACCATTGAACGGAAA
ATTCGAGACTTATGCGGTGATCAAGATTACATGAGTGTTTTAGAAGCTCAAAAAGATAAA
GTGGCAAAGCAAAATATGGAGTTGGCTCTTTTAGAGTCTTCGAAAACTACTTACAACAGC
TACATTGAGAAAATCAATGATGTGCCATGTTGTCCATTATGTAGTAAAGATTTCGAAATT
CAAGAGGCTGATGATCTTATAACTGAATTGAAAGAAAGCATCAGTAAACTTCCTGAGAAA
ATTGCACGTGTTCGAAAAGTTTTGCATACCGAAACACGCAAGTTTGATCAGTTGAACGAA
ATTAGACCTTCATATGAAAAATTGAAAGAACTCAAAAACGATAAAATAAATGCAGAGGAA
AAGCTCGTTAAGTTCGGACAAGATCTCTTGAAAAATGATGAATGCATAGATGACTTGGAA
TATTCTCTCACAGAACCTAAAGCGTTGTGTGATATGATAACAACAAGTGTACTTACTGAA
ATGATGAAATTAGACACTTTACAACGATCAATTAATAACAAAACTAAAGAGATTGATACC
ATCAAGTCCAACATGCCTAAAAATATTCCCAATATGAAATTAAGTGAAGCCATGGCAAAA
CGCAAAGAACTTTCGGAAAAGATTAAAAATAAAAATGAAACTGAAAGAAAACTCGAAAAG
GAAGTTAAAGAATACAACAACATGTTAATGGATGCTCGCGATGAATTAAATAATCTTCAA
GCACAAAAGAATGAGTATCAAACTAAAATGCAGGGTATTGAAAAATCGAAAGAAGAAATC
AAAAGATATGTGAAAGAAAATAAAGATTTAGAGCAACAACTTGCAGTTTCTGAACAGCAA
ATTGAGCCGCTTAAGAAGAAATTAGATACATTAATTCAGAAGAAAAAAGCTTGTCATGAT
GAAAATGAAGAAAAATTGCAACAGCAACAGATAACTATCAATCAATTAAAAGTAGATGAT
ACAAAAATTGATAATTTAAACAAACAAATTCGTGCACTGGAAAGTAAAAATCTTGAAGAA
AGAATTGATCAAACATCAAAAGACATAAAAACTATACAGCAGGAAATCAACATGGCTGAT
AAAAATTTCGAGGAGAAAGAAAATGAGATTCAAGAAATTCGAGATTTTTTGAATAAGGGT
GAAATAACTCTCTTCAATATTCAAGATAATATTATTATATTGAAGGTAGAAGAAGAACTC
AAGGCAGCAAAAGAAAAGTATTCAATTTTGAAAAAGACAATTGGTGATTTGGACCATGAA
AATATGGTTAAAGAAAAGAATCAAAACTCTGAAGAAATTGCAAAAATTTCTTCGTCGCGT
CAAAAACTCTTCGCCACAAAAGAGCTATTATATAAAACAATTGAAGAACACGAAAGAGAT
CTGAAGAAAGATCCTAAATTTAAAGATGCAAAGGCAAAATATCAAAAATCAATTGTTCAA
GAATGTGTTCTTCAACGAACTATTGATGATCTTAATAAATACCGTGCCGTACTAGAAAAA
GCTTTGCTTCAATTTCATCAAGAGAAAATGGATCAAATCAATCATACTGTCAAACAGTTG
TGGAATGATATTTACAAGGGAAATGACATAGATTTCATTATGATTAAAACAGACGAAGAA
GGTGCAACATCATCAGATAAGAAGAGAAGTTACAACTATCGAGTTGTTCAACAAAAACTT
GGAGGAGAATGGTCTGAAATGCGTGGTCGCTGTTCAGCAGGTCAAAAAGTTCTTGCATCT
CTCATTATTCGAATTGCTTTAGCTGACACATTCAGTGCAAAATGTGGAATTCTGGCACTC
GATGAACCGACAACAAATCTCGATCAGGTAAACATTAAAAGTTTGAGCAATGCTTTAGCT
CAACTTGTATCTCAACGTAATGATGGACGCTTTATGCTGATTGTCATTACTCACGATGAA
TCTTTTATTGCATCTCTCGATCAAACCGATATGTATTATCGTGTATCTCGTAATCATAAA
GGACTCTCTGTTATTGAAGAAGTAAGATATTAA

>g5624.t1 Gene=g5624 Length=1310
MSLLNKLHIQGIRSFGLDKEDEQRIEFTSPVTLIVGENGCGKTTIIECLKYALTGDVPPG
SDRGKNFIHESNLHANRTIFMGKVKLTVTDSQQVDKTVVRAMKLDNSKAKPKFETLNSSI
TFQHKNGQREDVSGRVDDINNYMCETMGVSKSILNNVIFCHQEDSNWPLDEGKKLKEKFD
AIFGTTEYNKAIDRIIKIRKEYQKQLAEIKGDIKYNAEIKSQVDKKERKIKELQAELNGV
DDKFKKLEDALIPLQEENLKILEKERNYSKHLSEQQNCRNIFNNKKDEYVKLQERITKNG
GKIDRDLESLKQQQLNFEKDRQDREKNKESLEEECKKLKSLKEKKRNDMMTLNGKMHEYT
SDYQRLQDIFAERFDKMQEICSKLNIPFTDDMDQSINTQSLADTLSNIKQYILSAEENFV
RLKAEAKKDEDAYQLNIDKIREERTKLETNIATQRNLIQEKTEIIAKLKREIASTESLIP
KLKEIQPQIEATEKKLKRLNDENNTEDMTLQQSLLQTEILELEDDQVKIDKSIEVLHSAS
QFTNELESKQKELTENQKEYTRLKNKSASNFKALFSNKDIENNFHHQMQAKQTELKKGIN
DVETKIKEKQHEKDRIIMERNNLRKTEEKLEDEIRTIERKIRDLCGDQDYMSVLEAQKDK
VAKQNMELALLESSKTTYNSYIEKINDVPCCPLCSKDFEIQEADDLITELKESISKLPEK
IARVRKVLHTETRKFDQLNEIRPSYEKLKELKNDKINAEEKLVKFGQDLLKNDECIDDLE
YSLTEPKALCDMITTSVLTEMMKLDTLQRSINNKTKEIDTIKSNMPKNIPNMKLSEAMAK
RKELSEKIKNKNETERKLEKEVKEYNNMLMDARDELNNLQAQKNEYQTKMQGIEKSKEEI
KRYVKENKDLEQQLAVSEQQIEPLKKKLDTLIQKKKACHDENEEKLQQQQITINQLKVDD
TKIDNLNKQIRALESKNLEERIDQTSKDIKTIQQEINMADKNFEEKENEIQEIRDFLNKG
EITLFNIQDNIIILKVEEELKAAKEKYSILKKTIGDLDHENMVKEKNQNSEEIAKISSSR
QKLFATKELLYKTIEEHERDLKKDPKFKDAKAKYQKSIVQECVLQRTIDDLNKYRAVLEK
ALLQFHQEKMDQINHTVKQLWNDIYKGNDIDFIMIKTDEEGATSSDKKRSYNYRVVQQKL
GGEWSEMRGRCSAGQKVLASLIIRIALADTFSAKCGILALDEPTTNLDQVNIKSLSNALA
QLVSQRNDGRFMLIVITHDESFIASLDQTDMYYRVSRNHKGLSVIEEVRY

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g5624.t1 CDD cd03240 ABC_Rad50 4 169 4.61847E-27
19 g5624.t1 CDD cd03240 ABC_Rad50 1206 1304 9.39672E-32
17 g5624.t1 Coils Coil Coil 216 250 -
14 g5624.t1 Coils Coil Coil 307 348 -
15 g5624.t1 Coils Coil Coil 412 509 -
9 g5624.t1 Coils Coil Coil 539 566 -
16 g5624.t1 Coils Coil Coil 599 647 -
13 g5624.t1 Coils Coil Coil 654 674 -
18 g5624.t1 Coils Coil Coil 748 768 -
11 g5624.t1 Coils Coil Coil 804 824 -
8 g5624.t1 Coils Coil Coil 834 927 -
12 g5624.t1 Coils Coil Coil 939 1009 -
10 g5624.t1 Coils Coil Coil 1033 1060 -
7 g5624.t1 Gene3D G3DSA:3.40.50.300 - 3 285 1.2E-33
6 g5624.t1 Gene3D G3DSA:3.40.50.300 - 1142 1301 2.8E-24
4 g5624.t1 PANTHER PTHR18867 RAD50 1 1309 1.4E-233
1 g5624.t1 Pfam PF13476 AAA domain 6 238 8.8E-33
3 g5624.t1 Pfam PF04423 Rad50 zinc hook motif 671 721 1.1E-8
2 g5624.t1 Pfam PF13558 Putative exonuclease SbcCD, C subunit 1188 1260 1.1E-6
21 g5624.t1 ProSiteProfiles PS51131 Rad50 zinc-hook domain profile. 647 743 9.532
5 g5624.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 22 1288 2.33E-25
22 g5624.t1 TIGRFAM TIGR00606 rad50: rad50 4 1305 1.4E-159

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5624/g5624.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5624.t1.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005634 nucleus CC
GO:0006281 DNA repair BP
GO:0030870 Mre11 complex CC
GO:0016887 ATP hydrolysis activity MF
GO:0000723 telomere maintenance 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