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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccatttttgctgattttgtgccaagctgacgtttcctatagatgtcacagtggtctctctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT

Basic information

species Zea mays
transcript GRMZM2G347808_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G347808_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g27930.1 (Oryza sativa), 3'ss of exon 11
-----------------------------------------------------------------------------------------------------gtaagcccatttttgctgattttgtgccaagc--tgacgtttcctatagatgtcacagtggtctctctctct---------gcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT-
                                                                                                      |   |  | || ||    ||   ||   | |  ||   ||| ||   ||||  | |||||||| |  || |         |||||| |||||||| |||||||| || |||||||||||||||||||| || |||||  | |||||| ||| |     |||  | |||| |||||||||| |   
gtatatccatttcctgtgatttgtgtatagctgacttggccacaaaagaagggttgatgcacttgtggagcttaattgtttatccatggtcttttcttctgatgcacttacttgtggaacttaattgtttatccatggtcttttcttctgatgcta-agtggtcttttcctattactttctggcagGTAGAGAAGAATTTCCTCAATGGGAAGCTGAAAGCCATAACAGCATATTTTGAGCAGCAGGATGGTTCAGATGTGCAG-GACGCTAGTGATACAAACCCCC
















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|32824820|gb|CD964542.1|CD964542
EST:     GATCTCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: GATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76015415|gb|DT942585.1|DT942585
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|89248734|gb|DY620520.1|DY620520
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|211522968|gb|FL454638.1|FL454638
EST:     GTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: GTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|71762989|gb|DR960926.1|DR960926
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76020625|gb|DT947795.1|DT947795
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|60394235|gb|DN227105.1|DN227105
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
EST: gi|76020624|gb|DT947794.1|DT947794
EST:     ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAG                         GTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT
genomic: ACCAATTGGCGGACATGTCCTTGTCTGTGGATCCCCCGTGGGCAGTTGAGgtaagcccat ... ctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgccaagctgacgtttcctatagatgtcacagtggtctctctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT
          agctgac  putative branch site (score: 3)
                                        tctctctctctgc  putative PPT
                       tatagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcccatttttgctgattttgtgccaagctgacgtttcctatagatgtcacagtggtctctctctctgcagGTCGAGAAGAACTTCCTCAACGGAAAGCTGAAAGCCATAACAGCTTACTTTGAAGAACAGGATCGTTGAACCAAGCATCGGCGCTGGTGATACAAATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC