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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatag

Basic information

species Zea mays
transcript GRMZM2G044819_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g14810.2 (Oryza sativa), 5'ss of exon 5
TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcgtcaaagtttctgggcttcattgatgaga----------actctaattcatgtttttgaatag
|||| |||||||| || || || ||||| ||||||||||| ||||| |||||||| |||||||||||||| ||||| |||||||| ||| |||||||||||||  | ||| |||||| ||||   || ||| | | |   | |||||          | ||| ||||||||   |||| ||
TTATGGATAAAGACAAAGGGAATTTGGTCAAAGCTGATCGTTTTGGTTACATTAAAAGGGCCATGCATGGCACCCAGATGCTTTCTACTAGTGCTGTGAGgtattgttaagacattttgtcagctttactgtggtcctgagctgagagaagataataaatcttattcatgtccatgaacag

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA13G17950.1 (Glycine max), 5'ss of exon 5
TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcgtcaaagtttc---tgggcttcattgatgagaactctaattcatgtttttgaatag--------------------------
| || || |||||||| || || ||||||||||||||||||||||| ||||| || || || |||||||| ||| ||||| | || ||||| ||||| |||||   || |  | | | |   |  | |    ||  | | | | || | |||    ||   | |      | ||                          
TCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGCACCAAAATGTTATCTACTCGAGCTGTTAGgtaagtgtcaggcttcttgctcacttgttatatgaacataagttatcaaaacatacatcattttaggctgacagaaatccatcttctaacataactctca

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA17G04580.1 (Glycine max), 5'ss of exon 5
TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcgtcaaagtttc---tgggcttcattgatgagaactc--taattcatgtttttgaatag------------------------
| || || |||||||| || || ||||||||||||||||||||||| ||||| || || || |||||||||||| ||||| | || ||||| ||||| |||||   || |  | | | |   |  | |    |   | | | |      ||||    ||  |||   |     |||                        
TCATAGACAAAGAGAAAGGCAATTTGGTTAAAGCTGATCGATTTGGTTACATAAAAAGAGCTATGCATGGTACCAAAATGTTATCTACTCGAGCTGTTAGgtaagtgtcagtcttcttgctcacctgttatatcaacataagttgcagtaacttatcaaaacatacatcactttaggctgacacaaatccatcttctaaa

upper sequence: GRMZM2G044819_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA15G21240.1 (Glycine max), 5'ss of exon 4
TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcg--tcaaagtttc-----tgggcttcattgatgagaactctaattcatgtttt---tgaatag-------------------
| || |||||||||   || || ||||||||||||||||||||||| || || || || ||||||||||| ||| ||||||| || || |||||||||||||    |      |||  |  ||  | |||      | |       ||  |||   |||  |  || | ||   |||| |                    
TGATAGATAAAGAGGGAGGCAATTTGGTTAAAGCTGATCGATTTGGTTATATAAAAAGAGCCATGCATGGAACCAAAATGCTATCTACGCGTGCTGTGAGgtcagtgctgagtattgtgattctgaattttgattatagaaagtcatgcagagtcttctcgtcaatttgttatatgaacataccctgcaaaaagtaacaa

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|148953072|gb|EE152549.2|EE152549
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAAGAATTGGTGGACCTGC
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGA-GAATTGGTGGACCTGC
EST: gi|17970200|gb|BM276964.1|BM276964
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|22935698|gb|BU571973.1|BU571973
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGGGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|26559582|gb|CA831817.1|CA831817
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         CGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|32937883|gb|CF042702.1|CF042702
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|71446139|gb|DR827189.1|DR827189
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
EST: gi|87156662|gb|DY401451.1|DY401451
EST:     ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAG                         TGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA
genomic: ATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaa ... ttttgaatagTGAAATATATGGAAGAGAATTGGTGGACCTGCGGAAAGAAATTCGATGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATTGATAAAGAGAAGGGAAACTTGGTTAAAGCTGATCGATTTGGGTACATTAAGAGGGCCATGCATGGTACCCAAATGCTTTCCACTCGTGCTGTGAGgtagaggtaacacatttcgtcaaagtttctgggcttcattgatgagaactctaattcatgtttttgaatag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG