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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaactactgtattgccag

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 4
TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaactac------tgtattgccag
||||||||||||| || || || ||||| |||||| |||| ||||||||||| | ||| |||||||| ||||||||| |    |  ||  |||  |||  ||   | | |||   ||| ||| ||  ||| | || || ||||| |       | |  | ||||
TGAAATATGAGGCTCGGCTTGAGGATGGCACTGTTATATCAAAGTCTGAGGGCGCTGAATTTACTGTTAAAGATGgtgattaccc-ataatct-ccttgtcaacatttcctgttcattattgagca-atcagctgcttgctaacgaaataaagtttggttccag
















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|148938868|gb|EC883219.2|EC883219
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTG
EST: gi|211429499|gb|FL195642.1|FL195642
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTG
EST: gi|149111770|gb|EE190920.2|EE190920
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
EST: gi|71767511|gb|DR965448.1|DR965448
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAA
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAA
EST: gi|47962115|gb|CN844824.1|CN844824
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
EST: gi|149081119|gb|EE170223.2|EE170223
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
EST: gi|148958573|gb|EC904817.2|EC904817
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCCTGGCCAA-GCTGTCAAAACCATGAAAAAGGCA
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCC-TGGCCAAAGCTGTCAAAACCATGAAAAAGGCA
EST: gi|149009170|gb|EE041295.2|EE041295
EST:     TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATG                         GCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG
genomic: TGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctct ... gtattgccagGCTACTTTTGTCCTGCCCTGGCCAAAGCTGTCAAAACCATGAAAAAGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAATATGAGGCCCGTCTGGAAGATGGTACTGTTGTATCCAAGTCTGAGGGGGTTGAGTTTACTGTGAAAGATGgtaaccctcttatgttctgtcttcacatggtcttctgaagatttttgtgcctatcggttgttttctaactactgtattgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG