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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagtacctcgtgatgctttgctcgccggattaattgaattgaatctgaatttgaactgtatattgcag

Basic information

species Zea mays
transcript GRMZM2G043893_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043893_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 5'ss of exon 2
GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCG--ACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagtac-ctcgtgatgcttt-gctcgccggattaattgaattgaatct----ga---atttgaactgtatattgcag-----------------
||   ||||    | ||| ||   ||   |  ||| | ||||| ||  | || | || |  |  |||    |||||||||||||| |||||| | ||||||||||||||  |   |||  | ||||||  || |      |  ||   ||   | |    ||   ||| | | |     ||| |                  
GCGCAGGCTCGCAGCGCCGCCGTTGCTCTCG-CCTCGCCGCCG-CCGGGTTGGGTTCAGGGAGAGGATCTTAGGCTGAATGCTGCTGCGGCAGTGGCTTCTGgtactgtgctgtgctccggttgctttcacttgtttttctttttccgttatctttttaggacccattcgcaataagcgttgaaattaactacttcccccat
















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|89247434|gb|DY619220.1|DY619220
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|148991872|gb|EE033466.2|EE033466
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|76913696|gb|DV165228.1|DV165228
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|149001042|gb|EE038291.2|EE038291
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAGA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|74236862|gb|DT644776.1|DT644776
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|148958193|gb|EC904398.2|EC904398
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71436982|gb|DR818032.1|DR818032
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71758309|gb|DR956246.1|DR956246
EST:     AATGCTGCCGCGGCAATTGCTTCTG                         GATCTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGAAAA
genomic: AATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71318207|gb|DR795866.1|DR795866
EST:     AGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: AGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|74236861|gb|DT644775.1|DT644775
EST:     AATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: AATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71774295|gb|DR972173.1|DR972173
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71318210|gb|DR795867.1|DR795867
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagtacctcgtgatgctttgctcgccggattaattgaattgaatctgaatttgaactgtatattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC