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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG

Basic information

species Zea mays
transcript GRMZM2G402242_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 5
gtactctttacttgcaagcctttcacatgtatctttaattcttcac---tccatcttcacagacaatccttttctat-gtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG
||| |  || |||||    ||||      | | ||  | |  | |    |  | ||| || | |||||||||| | | ||||||||| || ||||||||||||||| | |||| ||| |||||||| ||||| |||||||| ||||||||||||||||| || ||  |||| ||  | ||||
gtaattcttccttgcc--tctttggtgcattttttgtactacttataggttaagctttactgccaatcctttttttttgtagGCACTGGACCGAGGTGCTGCTCTCTTAAAAGTTGACAAGATTGTGACTGGACATAATGCTGATGACATTGCAGAAACTGTGTTATTGAATATATTACGTG

upper sequence: GRMZM2G402242_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 4
gtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG
||| |  ||||||||     |    ||  | | |   | |  |   |  | ||| || | |||||||||| | |  ||||||| || ||||||||||||||| | |||| ||| |||||||| ||||| |||||||| ||||||||||||||||| || ||  |||| ||  | ||||
gtaattcttacttgcctctttggtgcaattttttactagttataggttaagctttactgccaatccttttttct--agGCACTGGACCGAGGTGCTGCTCTCTTAAAAGTTGACAAGATTGTGACTGGACATAATGCTGATGACATTGCAGAAACTGTGTTATTGAATATATTACGTG
















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|74232164|gb|DT640078.1|DT640078
EST:     AATTGGTCTAAAAAACAATTTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: AATTGGTCTAAAAAACAATT-GTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
EST: gi|37416521|gb|CF645910.1|CF645910
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGA
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGA
EST: gi|91872707|gb|EB402664.1|EB402664
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
EST: gi|26558362|gb|CA830597.1|CA830597
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
EST: gi|87157289|gb|DY402078.1|DY402078
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
EST: gi|22472216|gb|BU036696.1|BU036696
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
EST: gi|50337086|gb|CO532212.1|CO532212
EST:     CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAG                         GCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG
genomic: CAATTGGTCTAAAAAACAATTGTACTTTCTGTGGAGTTTTTCGACGTCAGgtactcttta ... ttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG
         ctttaat  putative branch site (score: 4)
                                        tccttttctat  putative PPT
      tatctttaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactctttacttgcaagcctttcacatgtatctttaattcttcactccatcttcacagacaatccttttctatgtagGCACTAGATCGAGGTGCTGCTCTCCTGAAAGCTGATAAGATTGTAACTGGGCATAATGCAGATGACATTGCAGAAACCGTCTTGCTGAACATTCTGCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG