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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccctgcagctgcaatctatggagaccccatgcttcggatctccgatgccattgtgtcgtctgttaccattctaatcttacctcgcgaaaactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACAGTGTGCTGATAGTCGAAGAGAGGG

Basic information

species Zea mays
transcript GRMZM2G164265_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 16
gtatccctgcagctgcaatctatggagaccc---catgcttcg-gatctccgatgccattgtgtcgtctgttaccattcta-atcttacctcgcgaaaactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACAGTGTGCTGATAGT-CGAAGAGAGGG------------------------
||||          |||    || || | ||   | ||  | |  |    | |    | | | |||  | |     |||   | | || |  | |     || | |||| ||||||||||| ||||| |||||||| |||||||||| ||| ||||| || || |||  ||  |    |  ||                        
gtatatacattatcgcagctcattgaaatccggccgtgtcttgtaaaaaacaaacataatttctcgcgtttcggagttcagtaacatagccggtgtgctgttcgcagGATAAATGGGCGAAAAATCTGTACATAGCATCGATCTGCTTCGGGCGAACCGTCTGTTGACGGTGTGGCTGGCTGGCTGCCTTCCATTGAAGTTGAAGCG
















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|149102515|gb|EE287878.2|EE287878
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|149097990|gb|EE183935.2|EE183935
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148974692|gb|EE025499.2|EE025499
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|71430774|gb|DR811824.1|DR811824
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|149031683|gb|EE154868.2|EE154868
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|78113586|gb|DV531977.1|DV531977
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|149098314|gb|EE184284.2|EE184284
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148937186|gb|EC881367.2|EC881367
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148999277|gb|EE036205.2|EE036205
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148950556|gb|EC896133.2|EC896133
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|71764976|gb|DR962913.1|DR962913
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|71300237|gb|DR786190.1|DR786190
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148950415|gb|EC895982.2|EC895982
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
EST: gi|148939598|gb|EC884226.2|EC884226
EST:     AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAG                         GAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA
genomic: AGACGCAAGAAACCCTCCGGACCTCTGCCTTTCCCAGTTCACATGTCAAGgtatccctgc ... aactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatgccattgtgtcgtctgttaccattctaatcttacctcgcgaaaactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACAGTGTGCTGATAGTCGAAGAGAGGG
                        attctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccctgcagctgcaatctatggagaccccatgcttcggatctccgatgccattgtgtcgtctgttaccattctaatcttacctcgcgaaaactttgtagGAGAAATGGGCGAAGAATCTCTACATAGCCTCGATCTGCTACGGACGAACAGTGTGCTGATAGTCGAAGAGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG