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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccgtggccggtgctactccttcctctcgctatcgctgccgccttggtcgccgtcgccgtcgccgccgccgtggccacggtgacatcacatccc...

Basic information

species Zea mays
transcript GRMZM2G075333_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075333_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 5'ss of exon 1
CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgta--ccgtggccggtgctactccttcctctcgctatcgctgccgccttggtcgccgtcgccgtcgccgccgccgtggccacggtgacatcacatccc
||||||||||||||| || ||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||  |    || ||       || ||||||| ||||       || | || |   |  ||||||    ||   |||  |  ||   | |  ||  |  |  |
CGACGACGTCGTCGCCCTCCCCTACTCCTCCGGCACCACCGGCCTCCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCCCAGCAGgtgagccctccatgaatccctctcctccttcttctctgctctact-ctgcttccatttccgtcgtttccgagtccgg-gaagctgagctcgcagtagctgac
















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|148949767|gb|EC895250.2|EC895250
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAATCCGAACCTGTACTTC
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTC
EST: gi|91872377|gb|EB402334.1|EB402334
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGGACCCGAACCTGTACTTCCG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCG
EST: gi|148960512|gb|EE011113.2|EE011113
EST:     AGGGCGTCATGCTCACCCACCGCACCCTCATCACCAGCGTCGCGCAGCAG                         GGTGATGGCGAAAACCCGAACCTGTACTTC
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTC
EST: gi|148944630|gb|EC889762.2|EC889762
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTACTTC
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTC
EST: gi|74244018|gb|DT651932.1|DT651932
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTACTTCGGCAAGGACGACGTGGTGCTG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
EST: gi|76010779|gb|DT937949.1|DT937949
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGTTGCTG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
EST: gi|149100103|gb|EE186157.2|EE186157
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GGTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
EST: gi|148970851|gb|EE021627.2|EE021627
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTAC
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTAC
EST: gi|148969576|gb|EE020410.2|EE020410
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
EST: gi|71450118|gb|DR831168.1|DR831168
EST:     AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGAACCCGAACCTGTACTTCCGCA-GGACGACGTGGTGCTG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTG
EST: gi|76287909|gb|DV027477.1|DV027477
EST:     GGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAG                         GTTGATGGCGAGACCCCGA-CCTGTACTTCCGCAAGG
genomic: AGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGG

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), 44 (downstream exon)
Score: 14

CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTGTGCCTGCTGCCGCTGTTCCACATCTACTCGCTGAACTCGGTGCTGCTGG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 236

CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTGTGCCTGCTGCCGCTGTTCCACATCTACTCGCTGAACTCGGTGCTGCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTGTGCCTGCTGCCGCTGTTCCACATCTACTCGCTGAACTCGGTGCTGCTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 413

CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccg ... gaatatgaagGTTGATGGCGAGAACCCGAACCTGTACTTCCGCAAGGACGACGTGGTGCTGTGCCTGCTGCCGCTGTTCCACATCTACTCGCTGAACTCGGTGCTGCTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACGACGTCGTCGCGCTGCCCTACTCCTCCGGCACCACCGGGCTGCCCAAGGGCGTCATGCTCACCCACCGCAGCCTCATCACCAGCGTCGCGCAGCAGgtacgtaccgtggccggtgctactccttcctctcgctatcgctgccgccttggtcgccgtcgccgtcgccgccgccgtggccacggtgacatcacatccc

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