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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcacactaaaaagctgtccagaagctcatacaaacagggctgattcaagagcttctttccttgctttgagtattgatagatactgctagttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTGCCAAGAGAGGGCACTGCAACTAAGGCTGCACTTTTCTTCTGCCATGGAT

Basic information

species Zea mays
transcript GRMZM2G085438_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085438_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g49380.1 (Oryza sativa), 3'ss of exon 2
---tttcacactaaaaagctgtccagaagctcatacaaacagggctgattcaagagcttctttccttgctttgagtattgatagatactgctagttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTGCCAAGAGAGGGCACTGCAACTAAGGCTGCACTTTTCTTCTGCCATGGAT
      || |   ||  || ||    |   |||  |    | |     || ||  ||||||||  |   ||||  || | |   ||| ||||   |  |||||||||  || |||||||||||||| ||||| || |||||||||||||||||||| || ||||||||||| || ||||| ||||||||||||||||||||||
aaaagacaaatctaagtgcagtaggcactttcaatcttgaatgagctgtttaattgcttcttttttctttttg--tagtaagttatattgctttctg-tgtagAATTTTGAAACCAATTCAAAGGGGGTTGAGATTTTCTGGAAGAGTTGGCTGCCTAGGGAGGGCACTGCCACCAAGGCAGCACTTTTCTTCTGCCATGGAT
















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|71439067|gb|DR820117.1|DR820117
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|93016345|gb|EB641865.1|EB641865
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|71307182|gb|DR789758.1|DR789758
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|149076326|gb|EE164940.2|EE164940
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|78123599|gb|DV541983.1|DV541983
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|211083467|gb|FK983603.1|FK983603
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|71426297|gb|DR807347.1|DR807347
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|78082086|gb|DV510498.1|DV510498
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|78076593|gb|DV505027.1|DV505027
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|93015877|gb|EB641397.1|EB641397
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|37420223|gb|CF647800.1|CF647800
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|71439017|gb|DR820067.1|DR820067
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|78106711|gb|DV525129.1|DV525129
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|50333020|gb|CO528146.1|CO528146
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|148973073|gb|EE024135.2|EE024135
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
EST: gi|50329341|gb|CO524467.1|CO524467
EST:     ATGGCTCACAATGAAATCCAGATGGAAGAG                         AATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG
genomic: ATGGCTCACAATGAAATCCAGATGGAAGAGgtacgggcgt ... gttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaagagcttctttccttgctttgagtattgatagatactgctagttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTGCCAAGAGAGGGCACTGCAACTAAGGCTGCACTTTTCTTCTGCCATGGAT
                           tattgat  putative branch site (score: 3)
                           tattgata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcacactaaaaagctgtccagaagctcatacaaacagggctgattcaagagcttctttccttgctttgagtattgatagatactgctagttactgtagAATTACGAGACCAATTCAAAGGGCGTTGAAATATTCTGGAAGAGTTGGCTGCCAAGAGAGGGCACTGCAACTAAGGCTGCACTTTTCTTCTGCCATGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - acactaa
- - - - - - - - - - cagaagc
- - - - - - - - - - - - - - catacaa
- - - - - - - - - - - - - - - - - - - -ggctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgct