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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctttgtctctgaataatgtgatggctgttgttatttttatttttatttctaattgcctgtactttcattttatggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGGATCAATGATCTCAAG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 22
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|18649605|gb|BM498424.1|BM498424
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|4730484|gb|AI649650.1|AI649650
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|19822659|gb|BQ048683.1|BQ048683
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|20301651|gb|BQ164594.1|BQ164594
EST:     CCTGGTGACGCT-GAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: CCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     CAGCTNTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGCGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: CAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|18450492|gb|BM428770.1|BM428770
EST:     CTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: CTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|18649578|gb|BM498397.1|BM498397
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAAAAAGTAGTCTCCCGTTCAGTGACAG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGG-AGAAGTAGTCTCCCGTTCAGTGACAG
EST: gi|18450764|gb|BM429042.1|BM429042
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|18648832|gb|BM497651.1|BM497651
EST:     AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
EST: gi|18648721|gb|BM497540.1|BM497540
EST:     AGGCCTGG-GACGCT-GAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGG                         GTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG
genomic: AGGCCTGGTGACGCTCGAGCAGCTTTGAGGCGTTCGGTTAGGGAGAATGGgtttgttctt ... atggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttatttttatttttatttctaattgcctgtactttcattttatggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGGATCAATGATCTCAAG
                    ttctaat  putative branch site (score: 2)
     tatttttatttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctttgtctctgaataatgtgatggctgttgttatttttatttttatttctaattgcctgtactttcattttatggacatagGTCTGATATAGCAGAACAAAGTGGAGAAGTAGTCTCCCGTTCAGTGACAGGATCAATGATCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT