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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctctaaaccattcataaatcatgtacatctgcaggaactctcagctaatggtacactgtttacttcttgttattgtcatag

Basic information

species Zea mays
transcript GRMZM2G047509_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047509_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g14020.1 (Oryza sativa), 5'ss of exon 2
CATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctctaaaccattcataaatcatgtacatctgcaggaac-tctcagctaatggtacactgtttacttcttgttattgtcatag------------------------------------------------------------------------
||||||||||||||| ||||||||||  ||||  |||||  ||||| |||||||||| ||||||||||| |||||||| || |||| |||||| || ||||| |||| || ||||    || || | ||||   |   ||     |   ||| |  || | | | ||| ||       | |  | | |                                                                        
CATTTATGGGCATGCAACAGATGTGGAAATCACACCTTTAAATGAGGAGAAAGCTGTACAAGCTGCTACGGATCTCATTGGAGAAGGCTTTATTTTTTCGgtacttcacttaacctacaatgaaccttgtatgccaatagatttatagtagccacaggaata-tatttgctgggctgaagtaaccttgctctgttatgtgaaaaaataaagaaaataattgaaatatcaggaaatgaaacctgcatctttttggttttag
















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|211206703|gb|FL036107.1|FL036107
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|94478836|gb|EB707794.1|EB707794
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|44900751|gb|CK827296.1|CK827296
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCCGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|211206710|gb|FL036114.1|FL036114
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|32866858|gb|CF006540.1|CF006540
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|16377746|gb|BI992098.1|BI992098
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|211206707|gb|FL036111.1|FL036111
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGC
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGC
EST: gi|16927681|gb|BM080750.1|BM080750
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|148965768|gb|EE016647.2|EE016647
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|211206702|gb|FL036106.1|FL036106
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCT
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCT
EST: gi|13126108|gb|BG316558.1|BG316558
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|14243915|gb|BG841647.2|BG841647
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|211206704|gb|FL036108.1|FL036108
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|211206709|gb|FL036113.1|FL036113
EST:     AAGCTGTTCAAGCT-CTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCARAGAAACGCAAGGTCCGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|16925125|gb|BM078193.1|BM078193
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG
EST: gi|16918056|gb|BM073556.1|BM073556
EST:     AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCG                         GTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTTTGAG
genomic: AAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctct ... attgtcatagGTCGCTGTTGCTGCTCTAATTTTTGAGGTTCAGAGAAACGCAAGGTCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATTTATGGGCATGCCACAGATGTGGCGATCAGGCCTTTGGATGAGCAGAAAGCTGTTCAAGCTGCTACAGATCTCATCGGGGAAGCCTTTATCTTCTCGgtgcttctctaaaccattcataaatcatgtacatctgcaggaactctcagctaatggtacactgtttacttcttgttattgtcatag

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT