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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccataaagaatatcctctcagaaagcctattttttttagataatggaagctttattaatctcagtaaattctatcgagcttcattgaaaaagaattatcattgttaggattgctaacggttgcaatggtccag

Basic information

species Oryza sativa
transcript LOC_Os03g49600.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49600.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AC217401.3_FGT001 (Zea mays), 5'ss of exon 7
AAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccataaagaatatcctctcagaaagcctatttttttt---agataatggaagctttattaatctcagtaaattctatcgagcttcattgaaaaagaattatcattgttaggattgctaacggttgcaatggtccag
| ||||||||||||||||||||||||||||||||||||||  | |||||||| |||||||||||||||||||||||||| ||||| |||||  |||||||||||| | ||  |   |      ||| ||      ||||  |     || |||  ||| | || ||   ||| ||| |    | ||  | ||                                                  
AGGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTCACAAACTCAACCGAAGACCAAGCAGCGGCTCAAAGAGCAAGGGATTTCCATGTTGGTTGgtaag-ctatgcaagttccttgatcaaaacctgggttttcatgcaaggaaaatacaagttataatatcatcaataattgtctttga--tgcag-------------------------------------------------

upper sequence: LOC_Os03g49600.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G118003_T01 (Zea mays), 5'ss of exon 7
AAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccataaagaatatcctctcagaaagcctatttt---ttttagataatggaagctttattaatctcagtaaattctatcgagcttcattgaaaaagaattatcattgttaggattgctaacggttgcaatggtccag
| || |||||||| ||||||||||| ||||| || |||||| | |||||| |||| ||||||||||| || |||||||||||||||||||||||||| ||||||| | |||   | ||||||||   | | |||||| |   |||| |   |||  | |    | || | |||  || | |  |   |  |   |                                               
AGGTCGGAATAGTCCTGGACTTCAACTGGTACGAGGCTCTTACAAACTCACCTGATGACCAAGCAGCAGCCCAAAGAGCCAGGGACTTCCACATTGGCTGgtaag-ctatatc-agtatcctctgtcagaacctattctaagttttggtagatgagaac----taaaacacagctaactgttacatccgacgcag-----------------------------------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58686173|gb|CK074860.1|CK074860
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCA-GGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58679048|gb|CK067735.1|CK067735
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|428512|gb|D24663.1|D24663
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|218501129|gb|FG969556.1|FG969556
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATT
EST: gi|58662457|gb|CK051143.1|CK051143
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATT
EST: gi|163928475|gb|EG711363.1|EG711363
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|27576307|gb|CA999001.1|CA999001
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|27577942|gb|CB000637.1|CB000637
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|88212028|gb|CI211668.1|CI211668
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCAGTTGATAAATGGACATTACCCGCAGATAATGCAAGATC
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCA-TTGATAAATGGACATTACCCGCAGATAATGCAAGATC
EST: gi|58657255|gb|CK045935.1|CK045935
EST:     CAAGCAGCGGCTCAAAGAGCCA-GGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: CAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58678675|gb|CK067362.1|CK067362
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|29659818|gb|CB656093.1|CB656093
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|33675008|gb|CF303247.1|CF303247
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|218498123|gb|FG968220.1|FG968220
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATC
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATC
EST: gi|218482013|gb|FG963445.1|FG963445
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|40490189|gb|BX899802.1|BX899802
EST:     ACTGAAGAC-AAGCAGCGGCTCAAAGGGC-AGTGACTTC-ACATTGGTTG                         -TCTCTTGATCC
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCC
EST: gi|163928720|gb|EG711233.1|EG711233
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58664218|gb|CK052904.1|CK052904
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58680012|gb|CK068699.1|CK068699
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58668191|gb|CK056877.1|CK056877
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58679549|gb|CK068236.1|CK068236
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|33684672|gb|CF312911.1|CF312911
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|163919917|gb|EG714919.1|EG714919
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|3106636|gb|D42356.1|D42356
EST:     TGAAGACCAAGCAGCG-CTCAAAGA-C-AGGGGACTTCCACATTGGGTTG                         GTATCTTGA-CCATTGATAAATGGACATT
genomic: TGAAGACCAAGCAGCGGCTCAAAGAGCCAGGG-ACTTCCACATTGG-TTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATT
EST: gi|163923452|gb|EG709393.1|EG709393
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGC
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGC
EST: gi|218483773|gb|FG955251.1|FG955251
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGAGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58681508|gb|CK070195.1|CK070195
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATA
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATA
EST: gi|55827472|gb|AU032064.2|AU032064
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|58598612|gb|CK009140.1|CK009140
EST:     TCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGC-GGATCT
genomic: TCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|33676122|gb|CF304361.1|CF304361
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|86910403|gb|CI293058.1|CI293058
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACA
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACA
EST: gi|58671738|gb|CK060424.1|CK060424
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGCACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
EST: gi|27577236|gb|CA999930.1|CA999930
EST:     ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTG                         GTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT
genomic: ACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 72 (downstream exon)
Score: 176

AAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccat ... aatggtccagGTATCTTGATCCATTGATAAATGGACATTACCCGCAGATAATGCAAGATCTTGTGAAAGATAGGCTGCCCAAGTTCACTCCTGAACAAGCTAGATTGGTC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTTGGAATAGTTCTGGACTTCAATTGGTATGAAGCTCTTTCCAACTCAACTGAAGACCAAGCAGCGGCTCAAAGAGCCAGGGACTTCCACATTGGTTGgtaagaccataaagaatatcctctcagaaagcctattttttttagataatggaagctttattaatctcagtaaattctatcgagcttcattgaaaaagaattatcattgttaggattgctaacggttgcaatggtccag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA