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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgcatgatctacatctatatgcgtacgtgtgtgttctaagctagattgggctgccggctgtgctggagcttgagagatttctgggacgtgtgcag

Basic information

species Zea mays
transcript GRMZM2G086489_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 2
TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgcatgatctacatctatatgcgtacgtgtgtgt-tctaagctagattgggctgccg-gctgtgctg----gagcttgagagatttctgggacgtgtgcag
 | ||||| ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||| || |||||||  ||||  ||| ||  |||||| | | || ||||||| |     | | ||| || ||    ||   ||||| || | |||||| | || ||
GCGATGGCAGAGGAGGCGAGGGCGCGGTACGAGAAGGCGGTGTTCAAAGTTGTGGATCTGgtaattgtg-atgatcttgatctgcatgtgtttgtgtgtatgtgtatgctagatcgcctgtctgagctttggtgttaggaatctgagatatgtgtgggacatatgtag
















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|148941319|gb|EC886225.2|EC886225
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|22472411|gb|BU036891.1|BU036891
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|148961269|gb|EE011991.2|EE011991
EST:     GGAGGCGAGGGCGCGGTACGAGAAGGCCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: GGAGGCGAGGGCGCGGTACGAGAAGGCC-GTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|26558402|gb|CA830637.1|CA830637
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|22541992|gb|BU092430.1|BU092430
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|211095653|gb|FK967022.1|FK967022
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|211098118|gb|FK967027.1|FK967027
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|148940766|gb|EC885587.2|EC885587
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|148970820|gb|EE021584.2|EE021584
EST:     AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: AGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
EST: gi|19437265|gb|BM953675.1|BM953675
EST:     GGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTG                         GATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA
genomic: GGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAA

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: 432

TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 955

TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 781

TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1512

TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgc ... acgtgtgcagGATGACTATGCTCAGGAGGACGAGGAATACGAGGAGAAGCTGAAGAAGGAAACTGTGGTGCTGTTTTTCCTAGCAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCATGGCGGAGGAGGCGAGGGCGCGGTACGAGAAGGCCGTGTTCAAAGTGGTGGATCTGgtaattttgcatgatctacatctatatgcgtacgtgtgtgttctaagctagattgggctgccggctgtgctggagcttgagagatttctgggacgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA