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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGCTGTCAGCAAGAACATGGTGGAGAGTCTTGCTGTCCCGACCTTCAGGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatcttttcacaatctttaggaccaatgttttatgaatttgatgattggataaatgggtaatccttttttgcag

Basic information

species Zea mays
transcript GRMZM2G036534_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036534_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g08170.1 (Oryza sativa), 5'ss of exon 1
GGGTGCTGTCAGCAAGAACATGGTGGAGAGTCTTGCTGTCCCGACCTTCAGGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatcttttcacaatctt-------taggaccaatgtt-ttatgaatttg----atgattggataaatgggtaatccttttttgcag
|||||| ||||||||||||||||||||||| || || || ||||| ||||| || || |||||| |||| || ||||| || |||   |||||||| || ||||   | | |   | ||||       |  ||  | |  | ||||| | | |    ||| |||  |||||| || ||   ||||  |||
GGGTGCCGTCAGCAAGAACATGGTGGAGAGCCTCGCCGTGCCGACGTTCAGAGTCGGTTACACCTTCACAACCGATGCTCTGGATGCACTCTACAAGAAGgtgactgcctctgcaattcttgtttctcttagattagtactattatgcagtggtgggatggttgtgtaaatgagtgatg--ttttgacag
















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|78088435|gb|DV516828.1|DV516828
EST:     GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
EST: gi|93013412|gb|EB638932.1|EB638932
EST:     GGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
EST: gi|71431981|gb|DR813031.1|DR813031
EST:     GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
EST: gi|71444183|gb|DR825233.1|DR825233
EST:     GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
EST: gi|74236968|gb|DT644882.1|DT644882
EST:     GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
EST: gi|148932370|gb|EC876014.2|EC876014
EST:     GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACNNNNNN                         NTTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA
genomic: GGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatctt ... ttttttgcagATTAAGTCAAAGGGGGTTACAATGACAGCACTGTTGGCTAAGGCGACGGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGCTGTCAGCAAGAACATGGTGGAGAGTCTTGCTGTCCCGACCTTCAGGGTTGGGTACACCATCACGACTGATGCCCTCGATCAGCTCTACAAAAAAgtgagatcttttcacaatctttaggaccaatgttttatgaatttgatgattggataaatgggtaatccttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC