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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttatgcgtgctcaggcgcgcgcctgtctgattcgcctgaccctgtgattcgtggtgaataatttggctggttggaccttattgtgtgctcgtgttgcgtgttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG

Basic information

species Zea mays
transcript GRMZM2G144618_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144618_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 1
gtgcgttatgcgtgctcaggcgcgcgcctgtctgattcgcctgaccctgtgattcgtgg--tgaataatttggctggtt--ggaccttattgtgtgctcgtgttgcgtgtttta--tgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
               | ||  |      ||| |  ||    |  | ||  |||||||||   |  |  || |  |||||  |  | | ||   |   | |  |    |||| |   || |||| |||||||| |||||||||||||||||||| ||||||||
--------------gtaagatggctttttgttt--ttttgttatctcttcgattcgtggctcggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgttgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
















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|211507640|gb|FL212617.1|FL212617
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|71441642|gb|DR822692.1|DR822692
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCGACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|50322552|gb|CO517678.1|CO517678
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|211505290|gb|FL212613.1|FL212613
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|50322824|gb|CO517950.1|CO517950
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|71448550|gb|DR829600.1|DR829600
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|89761719|gb|DY689622.1|DY689622
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|71443863|gb|DR824913.1|DR824913
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|211507637|gb|FL212614.1|FL212614
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGATGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|93012223|gb|EB637743.1|EB637743
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|211507639|gb|FL212616.1|FL212616
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|76286410|gb|DV025978.1|DV025978
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|149014053|gb|EE043578.2|EE043578
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|211507638|gb|FL212615.1|FL212615
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGATGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
EST: gi|76017159|gb|DT944329.1|DT944329
EST:     CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGG                         AGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTGTACGACTTTGACACCGATGTCAACCAGTGGgtgcgttatg ... ttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaataatttggctggttggaccttattgtgtgctcgtgttgcgtgttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG
                                             ttttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttatgcgtgctcaggcgcgcgcctgtctgattcgcctgaccctgtgattcgtggtgaataatttggctggttggaccttattgtgtgctcgtgttgcgtgttttatgtagAGACGGAAGGACGTGGAGGGGTCGCTCTTCGTCGTCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG