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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactgcaacaccccggcctgtgatcctctctgtttcgtcccgatgcatgcaggtgttgttggctcggtttggttgtttgatcccggtaccatcttgtttcag

Basic information

species Zea mays
transcript GRMZM2G022777_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G022777_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 5'ss of exon 2
CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAG---------AAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactgcaacaccccggcctgtgatcctctctgtttcgtcccgatgcatgcaggtgttgttgg--------ctcggtttggttgt-----ttgatcccggtaccatctt---gtttcag
          |  |||||||||||||||||||||||||| |||||   ||||  |         |||||||| |||||| ||||||||||||||||||||||||||||||| |   | |        ||  |     |       |  | ||     |||||||||||||| ||||        ||||  |    |||     |||||||  |  |  | ||   |||||||
---------GCAGGAGCCGGAGCAGAACGGGCACGCCAATGGGGTGGCGAACGGGAGCGTCAGGAAGAGGACGTCCGATTTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtattt-ccgtgcgttagcgatcctcttttggtatggaatggtttgcgtgcatgcaggtgttcttggacaggcgtctcgtctcttgtgtagtccttgatcctcgatcggtgttgctgtttcag
















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|148995361|gb|EE034575.2|EE034575
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|91876817|gb|EB406774.1|EB406774
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211305002|gb|FL154237.1|FL154237
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACC-AGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|148933119|gb|EC876754.2|EC876754
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|31355560|gb|CD439917.1|CD439917
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|76933170|gb|DV173349.1|DV173349
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211305003|gb|FL154238.1|FL154238
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211305001|gb|FL154236.1|FL154236
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211165539|gb|FL456882.1|FL456882
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|78109695|gb|DV528111.1|DV528111
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|149080059|gb|EE169077.2|EE169077
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|110487038|gb|EE012240.1|EE012240
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|76280583|gb|DV020151.1|DV020151
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211131749|gb|FL468282.1|FL468282
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|30705707|gb|CD058888.1|CD058888
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211305004|gb|FL154239.1|FL154239
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|149106054|gb|EE291707.2|EE291707
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211307018|gb|FL154240.1|FL154240
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|71297616|gb|DR784759.1|DR784759
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211305000|gb|FL154235.1|FL154235
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGARACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|148963213|gb|EE014191.2|EE014191
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|78121929|gb|DV540313.1|DV540313
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|78106806|gb|DV525224.1|DV525224
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|76281419|gb|DV020987.1|DV020987
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|67021064|gb|CO449813.1|CO449813
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211307022|gb|FL154244.1|FL154244
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|149035101|gb|EE155087.2|EE155087
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|8367772|gb|BE050717.1|BE050717
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|148963079|gb|EE014036.2|EE014036
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|30307202|gb|CD001875.1|CD001875
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
EST: gi|211307019|gb|FL154241.1|FL154241
EST:     ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAG                         GCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT
genomic: ACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGAT

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: 164

CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGATGTCAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 110

CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGATGTCAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGATGTCAT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 95

CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactg ... cttgtttcagGCCAGGCAGACCCAGGTCCGAGCCGCCGCGATTCGCGACGGAGACGCTGATGTCAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAAGGAACCCGAGCCGGAGCAGAACGGGCACGCCAACGGGGTCCAGAACCAGAAGAGGACCTCCGATCTGGCGGTCTACGAGCAGTTCGAGCAGCAGgtgtggactgcaacaccccggcctgtgatcctctctgtttcgtcccgatgcatgcaggtgttgttggctcggtttggttgtttgatcccggtaccatcttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG