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_4 g16383 g16383.t1 TSS g16383.t1 9291967 9291967
chr_4 g16383 g16383.t1 isoform g16383.t1 9291996 9298248
chr_4 g16383 g16383.t1 exon g16383.t1.exon1 9291996 9292122
chr_4 g16383 g16383.t1 cds g16383.t1.CDS1 9291996 9292122
chr_4 g16383 g16383.t1 TTS g16383.t1 9292246 9292246
chr_4 g16383 g16383.t1 exon g16383.t1.exon2 9292585 9292655
chr_4 g16383 g16383.t1 cds g16383.t1.CDS2 9292585 9292655
chr_4 g16383 g16383.t1 exon g16383.t1.exon3 9292710 9292765
chr_4 g16383 g16383.t1 cds g16383.t1.CDS3 9292710 9292765
chr_4 g16383 g16383.t1 exon g16383.t1.exon4 9292824 9292959
chr_4 g16383 g16383.t1 cds g16383.t1.CDS4 9292824 9292959
chr_4 g16383 g16383.t1 exon g16383.t1.exon5 9293338 9293906
chr_4 g16383 g16383.t1 cds g16383.t1.CDS5 9293338 9293906
chr_4 g16383 g16383.t1 exon g16383.t1.exon6 9294420 9295669
chr_4 g16383 g16383.t1 cds g16383.t1.CDS6 9294420 9295669
chr_4 g16383 g16383.t1 exon g16383.t1.exon7 9296441 9298248
chr_4 g16383 g16383.t1 cds g16383.t1.CDS7 9296441 9298248

Sequences

>g16383.t1 Gene=g16383 Length=4017
ATGTTGAAAAAACTCTTCACTTTTATTTTTGTTTTGTTATTTGCATTTGCTATTGCTGCA
CCACAAAATCCACCTCCACCGCAAAATGGACAAGGACAAGGACCAAATGGACCACCAAGA
GGAAACTCAATGTCATTGCTCAATAAACTTTATATACAAGGTATTCGATCTTTTGGACTC
GATCGGGAAGATGAACAAAAAATTGAATTTACACCTCCTGTTACATTTATTGTTGGTGAA
AATGGAAGTGGAAAAACTGCAATAATTGAATGTTTAAAATATGCAATAACTGGTGATCTT
CCTTCTGGATCTGATCGAGGAAAAAGCTTTGTGCATGAATCATCTCTTTATAACAACCGT
GCAACTGTTGCTGGAAATGTCAAATTAACTGTGTCAAATTCACAAAATGTAAACCATACA
GTAACACGGTCATTAAAATTCAATGTTTCAGACAACAATAAACGTGATAAAAGAAAAATT
CAAGTTTCAATTACCAAACAAGAAGAAGATATAACATATTCAATTGATAATGCTGATACT
TACATGTGCAATGTTATGGGTGTTTCAAAATCAATTCTGAATAATGTAATTTTCTGTCAT
CAAGAGGATTCAAATTGGCCATTGGATGAAGGCAAAAAACTTAAAGAAAAATTTGATACA
ATTTTTGGTACAACACAATATAACAAGGCAATTGATAAAATCATAAAAATTCGTAAAGAA
TATCAAGAACAATTGAAAGACATTGAAAAAGATGTTGAAATTTATAAAGAAAGAATGCAA
CAAGTGAATAAAATTAAAAATAAAATTGAAACGCACCAAGCTGAACTTGATAAAAAAGAA
AATGAATGCAAAGAACTGAGTGAAAAACTACAAACACTTGAAAAGCAGAAGTCGGAAGTT
TTAGAAAAAGAAGAAAAATGCATTAAACTTAAAAATGAAAAAGTCATGATTAAAAATCTA
TATGAAACTAAAGCAAAAGATTATAAAAATCTTTCTGAAAAACTTACAAAAAATGAAAGT
AAAATGGAAGATGATTTGAAAATATTAACCGCACAACTAACAAATCATGAAAATGATAAA
AATAATCAAGCAAAATTGATGGAGTCTCTCGAAAAAGAATGCACTGAGCTCAAAAAATTA
ATGGAAGAAAATAGAAAAAATGTCGACATTTTAAAAGAAAAAAAGTTAAAATTTGAAGTT
GAATCTCAAAGTTTACAAAATCTTCTCAGTTTAAATTCTCAAAAGTTGAGAGAATTAAGT
TCAAAACTTAATATACCATTTGATGATGAAAATCAGTTAGCAAAAGGAATCGAGCAAGGA
ATTACACATGAAAAACAACATCTTCAATATTTAACTAAAGTTCGTATAGAAAACTCGGAA
ATAAATCAAAAAAATATTGATGACGTTCGTAAAAAATACACAAAACTAGAAGCAGAAATA
TCAATGCAGCAAAAGTTGATTAAAGAGAAAAATGAAAATATTGAAAAAATTACTCAAGAA
ATAGCAAATCTTGAAAATCAAATTTCTACATTTGAAGAAGTTGAAGTTAAAATTGAAACA
GTTGAAAAGAAGTTGAAAGAACTCAACGAAAGTAAAGAAATGGAAAAAATGAAGGCAAAT
CAAGAAAGTTTGCAAAATGAAATTTCAAATTTGGAAAATGCTCAAGCTGAACTTGATAAA
ATTATTGAATTTTTACTTTCTATTTCTCACTTAACTGCTGAACTTGATTCAAAGCAAAAA
GAAATAAATCAGAATATGAAAGAATTTGAAAACTTAAAAAGTGAATCTGAAACAATTTTT
GCTGTTCTGTTTCCTAATACGAAAATTGAGACAAAATTTCATCAACAAATACAAGAAAAA
CAAAAAGAATTGAAAAATTTCATTAATGAAATGGAAGCAAAAATTAAAGTAAAACAAAAC
GAAAATGATCGCTTTAAATTCGAATGTGACAGTTTACAAAAAACTGAAGAAAATCTTGAA
AATGATATTAAAAAAATTGAAGAAAACATTCGAAACTTATGCGGCGAAGAAGATTTTTCA
GACGTTTTTGAAGCTCAAAAGGAAAAAGTAGACAAAATGAAAATGGAACTAGCTCTCTTG
GAATCTTCGAAAAATTACAACAATAATTATATTGAGAAAATTAATAAAACTCCATGCTGC
CCTTTATGTTGCAAAAAATTTGAAAATGAAGAAGCAGAAAAAATGATCATCAAATTAAGA
GAAAGCAACAACCAACTGCCAGAAAAGATTGCAACTGTTCAAAGCAATTTAAAAGTTGAA
ACATTAAAATATGATAAATTGAATGAAATCAACCCTTCTTATAAAAATCTTCAAGAATTT
AAAAATAAAACTGAAATAATAAAAGACAAAATTAAGAACTTAGAAAAAAACATTGTTGAA
AATCAAAAAGAAATTGACAGTTTCAAAATTTCTATACGGAAACCTAAAGATTTATGTAAT
TTAATAACAACAAATGTTCACACGGATATGATGAAACTTGACAATCTACAGCAAGAAATA
ATCAAAAGAACATTGGAAATTGAAATCATCAAGTCTAAAATACCAGAAAATACTTCTGCA
ATAAAATTAGATGAAGCTCTTAAGAAACGCGGTGAAAATTCAGTAAATATTAAAATAAAA
AAGGTTGATTTAAAAACAGTTGACGATAAAATCAAAGAATATAATGAAACACTGATGAAT
ACTCGTATAGAACTTCAAAATCTTGAGATACAAAAAAATGAATACAAAAATAAACTTCAA
GAACTTGAAAAGCTCAAGAAAAATGCTGAAAAATTTAGAAATGAGAAGAGCAACTTGGAG
GGAGAACTGAAAACTTTTGAGCAACAAATTGAGCCATTAAAGACAAAACTGGAAGATTCC
ATTGCAAAAAAGAAAGCTTGTAATGAAGAAATCGAAACAAAAATTCAAGATCAACAAACA
AAAGTCAATGACCTAAATTTGAAAGAAAATGAAATTGAAAATTTGAAAAAACAAATTCAA
GCTCTTAAAAGTAAAAATTTAGAATGGAAAATTGATCAAATTTCAAATGATATGCAAGAA
AAAGAACAAAAAATTATTTTGGAACAAGAAAATTTAGAAAAGAAAGAAAGAAAAATTGAA
GAAATTCGAATAAACTTAGGTGAAAGTGATATGATTCTTTACAATATTCAAGATAATATT
TCATATCGTACTTTACAAAATGAAATTATAGAATACGAAGAAAAGCACACAAACATAAGA
AACTCAATTAGAGAACTCAACTATGAGCAAATCATTCAAGATAAAGAAAAAATCATTGAA
GAAATCACAAATATTTCATCAAAACAAAATCAACTTCTTGGTGAAACAAAATCTTTATCG
AATGCAATTGAAGAAAATGAAAAAGAACTAAAAGAAGACCTTAAATTGAGAAATGCAGAA
AAACAGCTTAAAAATTCTGTTTCTAAAGAAGAAGTTTTAAAATATACAATTGCAGACTTA
ACTGCATATCGAGCAATTTTAGAAAAAAAATTACTTCAATTTCATGAGGAAAAAATGGAG
CAAATAAATTCATCAATTAAACATTTATGGAATGAAATTTACAAAGGAAATGACATTGAT
TTTATTAAAATTAAAACCAATGAAGAAAATATAAAATCAACGGACAAAAGAAGAAATTAC
AATTATCGAGTTATGCAGCAAAAACTTGGTGGCGAATGGACAGAAATGCGTGGTCGTTGC
TCAGCTGGTCAAAAAGTTCTTGCATCATTAATAATTCGAATCGCTTTAGCTGACACTTTT
AGTGCCAAATGCGGAATTTTAGCACTTGATGAACCAACAACAAATTTGGATGAGAAAAAT
GTTAAAAGTTTGAGCAGAGCTTTAGCACGACTTGTGTCACAAAGAAACGATGGACGATTT
ATGTTAATAATTATTACTCATGATGAATCTTTTATTGCCTCACTTGATCAAGCTGACAAG
TATTATCATGTTTTCAATAATCGTGGAATTTCTAATATTGAAGAAGTTCGAAATTAG

>g16383.t1 Gene=g16383 Length=1338
MLKKLFTFIFVLLFAFAIAAPQNPPPPQNGQGQGPNGPPRGNSMSLLNKLYIQGIRSFGL
DREDEQKIEFTPPVTFIVGENGSGKTAIIECLKYAITGDLPSGSDRGKSFVHESSLYNNR
ATVAGNVKLTVSNSQNVNHTVTRSLKFNVSDNNKRDKRKIQVSITKQEEDITYSIDNADT
YMCNVMGVSKSILNNVIFCHQEDSNWPLDEGKKLKEKFDTIFGTTQYNKAIDKIIKIRKE
YQEQLKDIEKDVEIYKERMQQVNKIKNKIETHQAELDKKENECKELSEKLQTLEKQKSEV
LEKEEKCIKLKNEKVMIKNLYETKAKDYKNLSEKLTKNESKMEDDLKILTAQLTNHENDK
NNQAKLMESLEKECTELKKLMEENRKNVDILKEKKLKFEVESQSLQNLLSLNSQKLRELS
SKLNIPFDDENQLAKGIEQGITHEKQHLQYLTKVRIENSEINQKNIDDVRKKYTKLEAEI
SMQQKLIKEKNENIEKITQEIANLENQISTFEEVEVKIETVEKKLKELNESKEMEKMKAN
QESLQNEISNLENAQAELDKIIEFLLSISHLTAELDSKQKEINQNMKEFENLKSESETIF
AVLFPNTKIETKFHQQIQEKQKELKNFINEMEAKIKVKQNENDRFKFECDSLQKTEENLE
NDIKKIEENIRNLCGEEDFSDVFEAQKEKVDKMKMELALLESSKNYNNNYIEKINKTPCC
PLCCKKFENEEAEKMIIKLRESNNQLPEKIATVQSNLKVETLKYDKLNEINPSYKNLQEF
KNKTEIIKDKIKNLEKNIVENQKEIDSFKISIRKPKDLCNLITTNVHTDMMKLDNLQQEI
IKRTLEIEIIKSKIPENTSAIKLDEALKKRGENSVNIKIKKVDLKTVDDKIKEYNETLMN
TRIELQNLEIQKNEYKNKLQELEKLKKNAEKFRNEKSNLEGELKTFEQQIEPLKTKLEDS
IAKKKACNEEIETKIQDQQTKVNDLNLKENEIENLKKQIQALKSKNLEWKIDQISNDMQE
KEQKIILEQENLEKKERKIEEIRINLGESDMILYNIQDNISYRTLQNEIIEYEEKHTNIR
NSIRELNYEQIIQDKEKIIEEITNISSKQNQLLGETKSLSNAIEENEKELKEDLKLRNAE
KQLKNSVSKEEVLKYTIADLTAYRAILEKKLLQFHEEKMEQINSSIKHLWNEIYKGNDID
FIKIKTNEENIKSTDKRRNYNYRVMQQKLGGEWTEMRGRCSAGQKVLASLIIRIALADTF
SAKCGILALDEPTTNLDEKNVKSLSRALARLVSQRNDGRFMLIIITHDESFIASLDQADK
YYHVFNNRGISNIEEVRN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
28 g16383.t1 CDD cd03240 ABC_Rad50 47 208 4.4889E-26
27 g16383.t1 CDD cd03240 ABC_Rad50 1235 1324 2.82938E-30
19 g16383.t1 Coils Coil Coil 231 313 -
16 g16383.t1 Coils Coil Coil 318 401 -
13 g16383.t1 Coils Coil Coil 459 561 -
18 g16383.t1 Coils Coil Coil 568 595 -
14 g16383.t1 Coils Coil Coil 614 676 -
17 g16383.t1 Coils Coil Coil 683 703 -
21 g16383.t1 Coils Coil Coil 725 745 -
12 g16383.t1 Coils Coil Coil 777 811 -
15 g16383.t1 Coils Coil Coil 884 956 -
11 g16383.t1 Coils Coil Coil 968 1045 -
20 g16383.t1 Coils Coil Coil 1062 1089 -
10 g16383.t1 Gene3D G3DSA:3.40.50.300 - 46 327 1.6E-33
9 g16383.t1 Gene3D G3DSA:3.40.50.300 - 1050 1336 2.0E-27
4 g16383.t1 PANTHER PTHR18867 RAD50 44 1336 3.7E-217
1 g16383.t1 Pfam PF13476 AAA domain 49 296 7.3E-11
3 g16383.t1 Pfam PF04423 Rad50 zinc hook motif 704 750 1.6E-5
2 g16383.t1 Pfam PF13558 Putative exonuclease SbcCD, C subunit 1214 1289 4.6E-8
23 g16383.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
24 g16383.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
25 g16383.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
26 g16383.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
22 g16383.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 1338 -
31 g16383.t1 ProSiteProfiles PS51131 Rad50 zinc-hook domain profile. 676 772 9.408
5 g16383.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 65 1324 1.97E-25
6 g16383.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 66 569 1.62E-5
8 g16383.t1 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
29 g16383.t1 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 19 -
7 g16383.t1 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 19 -
30 g16383.t1 TIGRFAM TIGR00606 rad50: rad50 47 1325 5.8E-146

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: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