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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgtctgtctgtcatacttctccttgtgtctgtctatcttcggtcctttacataattgttcggcattgctttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG

Basic information

species Zea mays
transcript GRMZM5G846339_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 11
gttcgtctgtctgtcatacttctccttgtgtct---gtctatc---ttcggtcctttacataattgttcggcattgctttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG
||| || | ||      |  ||   | || |||   | | ||    ||   | ||| |  || ||| | |   |   ||     |||||| |||||||||||||| |||||| | |||||||| ||||||||||| ||||||
gtttgtatttcatagtaagctcaattagtatcttcgggccattcattttttttcttcatttatttgattgtgttaatttcctctgcagAATGACTTGGTTCATGGATGGGGCCTTGATTTTGCTCTCAGGAAATGCGTGGAG
















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|148929009|gb|EC874209.2|EC874209
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|148945517|gb|EC890762.2|EC890762
EST:     AAGAGATGCATGGAAGGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: AAGAGATGCATGG-A-GATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|211435723|gb|FL461646.1|FL461646
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|211015300|gb|FL437092.1|FL437092
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|211501409|gb|FL138835.1|FL138835
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|44682283|gb|CK787331.1|CK787331
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
EST: gi|149070556|gb|EE158958.2|EE158958
EST:     CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAG                         AACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG
genomic: CTCCAGTCTTCTCAAGAGATGCATGGAGATGTGTGTGGCATATGATTCAGgttcgtctgt ... ttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtctgtctatcttcggtcctttacataattgttcggcattgctttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG
                                        ttgcttt  CT-rich tract
                     tttacataattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgtctgtctgtcatacttctccttgtgtctgtctatcttcggtcctttacataattgttcggcattgctttggacgcagAACGACTTGGTTCATGGTTGGGGCTTGGATTTTGCGCTCAGGAAATGTGTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG