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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagccatatattctcattcaaatatcattatttatctcttctgcttaatactgacaaaggtgtaatagtatttttttagtattgatttgtc...

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 5'ss of exon 8
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagccatat-attctcattcaaatatcattatttatctcttctgcttaatac-tgacaaaggtgtaatagtatttttttagtattgatttgtc
||||||||||||||||| ||||||||| |||||||||||||||||||||||||||| ||||| |||||||| ||||| |||||||| || |||||||||||| |||| |||| | ||  | ||  ||||| ||| || | | ||||||  | | ||  |||  | | |||  |    ||| | |   |||  ||| | 
GTTGATGATACTGAAGTTATCAGTTTTCTGCTGCAAACTGAAATAATTCCTCTGTGTTTGCGTACCATGGAAATGGGAAGTGAGCTGTCAAAAACTgtatgtcgctaaccatctcatgtttatctaaataccatcatctttttcttct-ttaagtatgtgatgatgctgtc-tgaagtttgtgtgtaatttttttttt

upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G43220.1 (Glycine max), 5'ss of exon 6
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgt--atgtagctagccatatattctcattcaaatatcattatttatctcttctgcttaa-tactgacaaaggtgtaatagtatttttttagtattgatttgtc
||||||||||| ||||| || |||||  | ||   ||| || |||||||| |||||| |||| |||||||| ||||| ||||| ||||||||||| ||  |  |  ||     | |||||| | ||     | |  | ||||  | ||   ||   |  | |      | || |     |||  |  |    ||||   
GTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCCCTGTGCCTGCGCACCATGGAAATGGGCAGTGAACTATCCAAAACAgttgagttttctgattctttattcttagtctttggtga--acttatgccatcacattgtctggtaaattgaatttagtttccatttcctcctccatatttaa-

upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA18G10400.1 (Glycine max), 5'ss of exon 6
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagccatatattctcattcaaatatcattatttatctcttctgcttaatactgacaaaggtgtaatagtatttttttagtattgatttgtc------
||||||||||| ||||| || |||||  | ||   ||| || ||||||||||| ||||||||||||||||| ||||| ||||||||||||||||| || ||    ||   ||   |  ||||||     | |  | ||||  | ||   ||| | |||  |||   |   || | |   |||  |    |||| |       
GTTGATGATACAGAAGTTATAAGTTTCCTTCTTTCAACAGAGATAATTCCTCTATGCTTGCGAACCATGGAAATGGGCAGTGAGCTATCCAAAACAgt-tgagtttactgat---tcttcattctttggtaa--acttatagcatcacattatttctggtaaattggatttattttccatttcctccctatttctttgagct

upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT3G20800.1 (Arabidopsis thaliana), 5'ss of exon 6
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagccatatattctcattcaaatatcattatttatctcttctgcttaatactgacaaaggtgtaatagtatttttttagtattgatttgtc---
||||||||||| || ||||| || ||  | ||   ||||||||| |||||||||||| | || |||||||| ||||| |||||||| || ||||| ||| ||   |     ||   |  ||||   || |   |||   |  |||||  ||||   |    |  || | | | |   ||||   |    ||||||    
GTTGATGATACAGAGGTCATTAGCTTCCTTCTTTCAACTGAAATTATTCCTCTGTGCCTCCGTACCATGGAAATGGGGAGTGAGCTGTCAAAAACAgtaagtcttttaatttaccgttacattttcatgttcatatg-gtaccttct--ttaagtttcttgacagtcttaaaattcgttttagatgcacatttgttagt

upper sequence: GRMZM2G045331_T01 (Zea mays), 5'ss of exon 7
lower sequence: PP1S276_27V6.1 (Physcomitrella patens), 5'ss of exon 6
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagc--catatattctcattcaaatatcattatttatctcttctgcttaatactgacaaaggtgtaatagtatttttttagtattgatttgtc--
|| ||||| |||||||| || | |||  | |||  ||| || || |||||||||||| | ||||| ||||||||||| ||||| |||||||| || ||  ||| |  ||  ||   ||  ||  |||| |||  |||   |  |      | || ||   | |  |||   |   | | |  ||||| ||| |    |  
GTGGATGACACTGAAGTTATTAATTTCCTACTGTCAACCGAGATTATTCCTCTGTGCCTACGAACGATGGAGATGGGAAGTGAACTATCCAAGACAgtgagtaccctgctccacggatgttccctcaa-tattgtta--caagttcgaaacatagtagaaa-attggttggaagatttatgattagttttgttgatacga

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|32868505|gb|CF008187.1|CF008187
EST:     TCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
genomic: TCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|211200410|gb|FL096663.1|FL096663
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCAAAAGATTCTTCTARATGATGTTGGGCTGCGC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|78091209|gb|DV519583.1|DV519583
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCCAAAGATTCTTCTAGATGATGTTGGGCTGCGC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|71445883|gb|DR826933.1|DR826933
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCAAAAGAT-CTTCTAGATGATGTTGGGCTGCGC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|31356490|gb|CD440847.1|CD440847
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|76936740|gb|DV174858.1|DV174858
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCA
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCA
EST: gi|31354815|gb|CD439172.1|CD439172
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCCTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCCC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC
EST: gi|74233595|gb|DT641509.1|DT641509
EST:     TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACT                         GTGGCAACTTTCATCGTCCNAAAGATTCTTCTAGATGATGTTGGGCTGCGC
genomic: TTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagct ... gcatatgcagGTGGCAACTTTCATCGTCCAAAAGATTCTTCTAGATGATGTTGGGCTGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGATACTGAAGTCATCAGTTTTTTGCTGCAAACTGAAATAATTCCTCTGTGCTTGCGAACCATGGAGATGGGTAGTGAGCTATCCAAAACTgtatgtagctagccatatattctcattcaaatatcattatttatctcttctgcttaatactgacaaaggtgtaatagtatttttttagtattgatttgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG