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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgatacgcattttccggttctgcttctgttctatatttgctccctgtaccgagttcacgcatttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG

Basic information

species Zea mays
transcript GRMZM2G017941_T01
intron # 6
splice site 3'
intron type U2

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|149084465|gb|EE173923.2|EE173923
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAAAAACAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|71329488|gb|DR801466.1|DR801466
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|211169629|gb|FL169502.1|FL169502
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|60401365|gb|DN234172.1|DN234172
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|211171319|gb|FL169525.1|FL169525
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|7242261|gb|AW574447.1|AW574447
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|149013784|gb|EE043248.2|EE043248
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAAT
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAAT
EST: gi|31358873|gb|CD443230.1|CD443230
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|93281025|gb|EB673289.1|EB673289
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|71329487|gb|DR801465.1|DR801465
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|78106618|gb|DV525036.1|DV525036
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|101399852|gb|EB821772.1|EB821772
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|211172988|gb|FL169531.1|FL169531
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCTACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|211172990|gb|FL169533.1|FL169533
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|67024634|gb|CO453383.1|CO453383
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|13515991|gb|BG518267.1|BG518267
EST:     CCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|149072392|gb|EE160666.2|EE160666
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCCACCCGAGTGGACAGACTGATGTAAT
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAAT
EST: gi|148982778|gb|EE028604.2|EE028604
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
EST: gi|37397410|gb|CF636002.1|CF636002
EST:     CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAAT                         GACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC
genomic: CCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATC

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

CTGTAAAAGTGGTTTTGGAAGAAACCGTATCACCTACACAGACACGTGCGCCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 214

CTGTAAAAGTGGTTTTGGAAGAAACCGTATCACCTACACAGACACGTGCGCCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

CTGTAAAAGTGGTTTTGGAAGAAACCGTATCACCTACACAGACACGTGCGCCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 276

CTGTAAAAGTGGTTTTGGAAGAAACCGTATCACCTACACAGACACGTGCGCCGTGAGTGGCCAAGATCTGAAGACGTATCACAACATGGATGCTATCAATgtaagtcgat ... atttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttctgcttctgttctatatttgctccctgtaccgagttcacgcatttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG
                                            cattttt  CT-rich tract
             ttctatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgatacgcattttccggttctgcttctgttctatatttgctccctgtaccgagttcacgcatttttgcagGACTTGGTAGTGTCAGGAAGAACCAACCCGAGTGGACAGACTGATGTAATCGTCTTCTGCAGCGGCGGGTTCGAGAAGTTAGGCACCACGGAATCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT