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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccactcctactccctgcctgctgtgcgaaatcgagcacccaaaaccctaatttaaggatattttatttcttcgacctttttgcaaaaaaaaaaaaaacatcgtgcggtggtctgccttggctgcagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC

Basic information

species Zea mays
transcript GRMZM2G472991_T03
intron # 2
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|93016530|gb|EB642050.1|EB642050
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|20299997|gb|BQ162940.1|BQ162940
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|20300018|gb|BQ162961.1|BQ162961
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|76014878|gb|DT942048.1|DT942048
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCC
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCC
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCC
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCC
EST: gi|89106284|gb|DY576501.1|DY576501
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|22489226|gb|BU049149.1|BU049149
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|91056420|gb|EB166838.1|EB166838
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|18383990|gb|BM417190.1|BM417190
EST:     CGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGTGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: CGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AGAAG--GA-GG---ACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
EST: gi|211277358|gb|FL192926.1|FL192926
EST:     ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAG                         CCAGCAGCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA
genomic: ACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagC-AG-A--AG--G-AGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTA

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 6

GCGCTGTCTCTGTCCTCATCTCCGCGAAGACAGGCTACCGCCGCCGCCCTACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 7

GCGCTGTCTCTGTCCTCATCTCCGCGAAGACAGGCTACCGCCGCCGCCCTACGCCAGGTGCCGAGGCCTCTCTGTCTCTTCGCCGGCGACGATCCAATAGgtatttccac ... cagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcaaaaaaaaaaaaaacatcgtgcggtggtctgccttggctgcagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC
     aaaaaaaaaaaaaaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccactcctactccctgcctgctgtgcgaaatcgagcacccaaaaccctaatttaaggatattttatttcttcgacctttttgcaaaaaaaaaaaaaacatcgtgcggtggtctgccttggctgcagccagcagCAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG