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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc...

Basic information

species Zea mays
transcript GRMZM2G027105_T06
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027105_T06 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g39720.3 (Oryza sativa), 5'ss of exon 2
AGGCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc-
 |   |  |||||||||||||| ||||| ||||||||||||||||| || |||||||||||||||||||||||||||||  |||||||||||||||||||||| ||     |||     ||  |    |     || | | | | ||||     |  |     |  | || || ||  ||| |  |  ||   | |  |  
CGAGCGCGCTCATGGCTCGCGTGTACGTGGGGAACCTGGATCCGCGCGTGACGGCGCGGGAGATCGAGGACGAGTTCCGCGTGTTTGGGGTTCTGAGGAGgtgtgagattctgctgactctgagctaagaatcactatatatatatattttactccctgtgttgcgtatacttgtttaatg-tgcctgcttgttcgtttga

upper sequence: GRMZM2G027105_T06 (Zea mays), 5'ss of exon 1
lower sequence: EFJ27548 (Selaginella moellendorffii), 5'ss of exon 1
AGGCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc
           ||||| ||||||||||| || || |||||||||||    |||| ||||||| ||||||||||||||||||  || || || ||| | |||| ||   ||    |     |||    | |||  | |  |||||  |  |  |  |  |   | ||| |     |     |||||  | || |       
-----------ATGGCGCGCGTCTACGTCGGCAATCTGGATCCGCGATCGACGGAGCGGGAGCTCGAGGACGAGTTCCGGAGCTTCGGCGTGCTGCGAAGgtaagccacg----cgcaaatcgattctcctct-cgtcctttttccagcgcca--aagaatccaaatctgaggctc----gattttgc-tggcag-----

upper sequence: GRMZM2G027105_T06 (Zea mays), 5'ss of exon 1
lower sequence: EFJ35719 (Selaginella moellendorffii), 5'ss of exon 1
AGGCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc
           ||||| ||||||||||| || || |||||||||||    |||| ||||||| ||||||||||||||||||  || || || ||| | |||| ||   ||    |     |||    | |||  | |  |||||  |  |  |  |  |   | ||| | |   |     |||||  | || |       
-----------ATGGCGCGCGTCTACGTCGGCAATCTGGATCCGCGATCGACGGAGCGGGAGCTCGAGGACGAGTTCCGGAGCTTCGGCGTGCTGCGAAGgtaagccacg----cgcaaatcgattctcctct-cgtcctttttccagcgcca--aagaatccaaatctggggctc----gattttgc-tggcag-----

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|94479705|gb|EB708663.1|EB708663
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15323604|gb|BI478888.1|BI478888
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGA
EST: gi|91874373|gb|EB404330.1|EB404330
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|18384999|gb|BM418198.1|BM418198
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGTCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|33467938|gb|CF244987.1|CF244987
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|211082660|gb|FL069456.1|FL069456
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|15313695|gb|BI478910.1|BI478910
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|13557662|gb|BG549018.1|BG549018
EST:     GGTCGCGGGTAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGG
genomic: GG-CGCGGG-AGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGG
EST: gi|149083666|gb|EE173012.2|EE173012
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
EST: gi|50327964|gb|CO523090.1|CO523090
EST:     ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAG                         TGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA
genomic: ACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcg ... ttccatgcagTGTATGGGTTGCTAGGAAACCACCAGGGTTTGCCTTCATTGACTTTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCTGAACTCATGGCTCGCGTCTACGTTGGGAACCTGGATCCGCGTGTCACGGCGCGGGAGATCGAGGACGAGTTCCGGATGTTTGGGGTTCTGAGGAGgtgagatgcggtgcctttgctcggaagtgctcagctttgtttttttattgatagcagtagcgcgaatgtagtttttctatgatttcccctgacttgcctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG