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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtgtcccctgggatcgtcagattttcctctgagagaaacgaaatgctatttcctgttattctacgagtattgcgtccagattttccaagccgt...

Basic information

species Zea mays
transcript GRMZM2G348512_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G348512_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g45274.2 (Oryza sativa), 5'ss of exon 4
CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgt---gtcccctgggatcgtcagattt--tcctctgagagaaacgaaatgctatttcctgttattctacgagtattgcgtccagattttccaagccgt
||||||||||||||| |||||||| ||||||||   |||| | ||||||||||| ||    ||||  |     |   | ||||  || |||  |   |       || |   || |  |      |||| || ||   |    | |   |||  
CAAGAAGCCGGAGCTCTTCGAGCCGCTCAAGGCCGGCCAGGCACCCAAGgtacgctgctccgtccatttcctgctcaaaatttgttcttctttgtctactagtgagccaac-ccagccagctg--gagttttacggttactcctccatggcc--
















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|211134693|gb|FL266946.1|FL266946
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|149089209|gb|EE178408.2|EE178408
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|149111605|gb|EE190745.2|EE190745
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|6021522|gb|AW066450.1|AW066450
EST:     TCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: TCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211134695|gb|FL266948.1|FL266948
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|5928883|gb|AW056175.1|AW056175
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211134692|gb|FL266945.1|FL266945
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211134691|gb|FL266944.1|FL266944
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211134689|gb|FL266942.1|FL266942
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|78180753|gb|DV551126.1|DV551126
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211134690|gb|FL266943.1|FL266943
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|12046395|gb|BF728534.1|BF728534
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|149098353|gb|EE184327.2|EE184327
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|149009135|gb|EE041274.2|EE041274
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
EST: gi|211402419|gb|FL355661.1|FL355661
EST:     CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAG                         TACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG
genomic: CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTG

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 3 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 78

CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCACCCCGGCGAGGCCTTTGCCGTCCGCAACATCGCCAGCATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 89

CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCACCCCGGCGAGGCCTTTGCCGTCCGCAACATCGCCAGCATGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 61

CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtg ... atgcatgcagTACATGGTGTTCGCCTGCTCCGACTCCCGCGTGTGCCCGTCGGTGACCCTGGGCCTGCACCCCGGCGAGGCCTTTGCCGTCCGCAACATCGCCAGCATGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAAGCCGGAGCTGTTCGAGCCACTCAAGGCGCACCAGTCGCCCAAGgtacggtgtgtcccctgggatcgtcagattttcctctgagagaaacgaaatgctatttcctgttattctacgagtattgcgtccagattttccaagccgt

 AAGAAG
- AGAAGC
- - - -  GGAGCT
- - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacgaa