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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattcctcccatttttatggtcaatggatgctattcctcatccagaatcatgatttaaatattcatctgagatgatattcttgagcttttttgcag

Basic information

species Zea mays
transcript GRMZM2G119791_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119791_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g36420.1 (Oryza sativa), 5'ss of exon 3
GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattcc-tcccatttttatggtcaatggatgctattcctcatccagaatcatgatttaaatattcatctgagatgatattcttgagcttttttgcag
|| || || |||||||| ||||||||| ||||||||||||| |||||||| ||||||| ||||||| |||| ||||||||||| ||||| |||||||| |  ||| || |    || |   | || ||         |  || |     |||  | ||    ||||   | |  |      || |||||
GCAAGAAGGGGACTTGGCCTCACAGCAGATATTATTGATCATTGCAAGCTAGTCCTTAGATTTCCTAAAGGAACCAACAGCACTTGGgtaagtattccctgtcatgttcacatgcagttacttctgttaacggatttgtgtccttcaacaaaggtccactcaagatatcacttctcttgacttatgcag

upper sequence: GRMZM2G119791_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G27570.2 (Glycine max), 5'ss of exon 3
GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattcctcccattttta-----tggtcaat---ggatgctattc----ctcatccagaatcatgatttaaatattcatctgagatgatattcttgagcttttttgcag
| || ||| || ||||| ||||| ||||||||||||||||| |||||| |  | |||||||  |||||||| ||||||||||| |||||  || |   ||    || |      ||   | |   | ||   ||||      |||  | || ||     | | | ||  | |    |   ||  |||    |  ||||||
GATAACAGGGGGCTTGGACTCACTGCACATATTATTGATCATTGCAAGTTAATTCTTAAATACCCTGAAGGTACCAACAGCACTTGGgtatgtctctttctgccttctgaatcctgagtagtcttgaatttgattcaatttccattaataaccaattgctgattttttgtttacttttcaatgtttgga--taattgcag

upper sequence: GRMZM2G119791_T03 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G05340.1 (Glycine max), 5'ss of exon 3
GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattcctcccattttta-----tggtcaatggatgctattcctc-atccagaatc-atgatttaaatattcatctgagatgatattcttgagctt-ttttgcag-----------------
| || ||| || ||||| ||||| |||||| ||||||| || |||||  |  |||||||||  |||||||| ||||||||||| |||||  || |   ||    || |      ||     ||    || ||  |  || ||   || || | ||  | |||   ||||  |  | || ||  | || |||| ||                  
GATAACAGGGGGCTTGGACTCACTGCACATGTTATTGACCATTGCAAATTAATCCTTAAATACCCTGAAGGTACCAACAGCACTTGGgtatgtctctttctgccttgtgaatcctgagttctgagcactcttatttgattcaatttccattaattgcaaattg--ctgatttttttttttttggtttatttttcaatgtgtcaatgattgcag

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|71436803|gb|DR817853.1|DR817853
EST:     ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG                         TATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
genomic: ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattc ... ttttttgcagTATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
EST: gi|211356321|gb|FL081349.1|FL081349
EST:     ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG                         TATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
genomic: ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattc ... ttttttgcagTATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
EST: gi|211356320|gb|FL081348.1|FL081348
EST:     ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGG                         TATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
genomic: ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattc ... ttttttgcagTATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
EST: gi|78082688|gb|DV511091.1|DV511091
EST:     ATCACTGCAAGCTGGTCCTTAACTTTCCTGAAGGGACCAACAGCACCTGG                         TATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC
genomic: ATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattc ... ttttttgcagTATAATGCTCAGTTCAAGATTTTTGAACCTCTAGAATACAAATATGATGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAGCAGAGGACTTGGTCTCACAGCACATATTATTGATCACTGCAAGCTGGTCCTTAAATTTCCTGAAGGGACCAACAGCACCTGGgtcagtattcctcccatttttatggtcaatggatgctattcctcatccagaatcatgatttaaatattcatctgagatgatattcttgagcttttttgcag

- - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG