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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actattagtggcttcgtgatataccaatatgtgacaaaatagttgatgacacgagcatctaaatggaactcaatttcatgtgttgactctttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGAGCAGCACGCCAGTGGTCGACGGGGGGTTGTTCCATCATAATCATATTAC

Basic information

species Zea mays
transcript GRMZM2G390076_T03
intron # 3
splice site 3'
intron type U2

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|69351419|gb|DR452128.1|DR452128
EST:     CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTCAAG                         TCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|30052497|gb|AI065786.2|AI065786
EST:     CTGCGAGGAAGGTGTNGGGTGGTTCAAATAATAACAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGNTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|93284121|gb|EB676385.1|EB676385
EST:     CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|37384218|gb|CF629167.1|CF629167
EST:     CTGC---GAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|116822684|gb|EC866106.1|EC866106
EST:     TGCGAGGAAAGGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTCAAG                         TCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: TGCGAGG-AAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|211195637|gb|FL445841.1|FL445841
EST:     GGTGTTGGGTGGTTCAACTAAWTAACAAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATAYCAGGTTGGTTGGTGA
genomic: GGTGTTGGGTGGTTCAACTAA-TAAC-AAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|16379645|gb|BI993074.1|BI993074
EST:     CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
EST: gi|6695722|gb|AW288800.1|AW288800
EST:     CTGCGAGGAAAGTGTTGGGTGGTTCAACTAATAACAAATCTGGCTTCAAG                         TCATTGAGAGGATGGTGACAATGGCAAGCCTGATATCAGG
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGG
EST: gi|60359288|gb|DN226261.1|DN226261
EST:     CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAG                         TCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA
genomic: CTGCGAGGAAGGTGTTGGGTGGTTCAACTAATAACAAATCAGGCTTCAAGgtatacatca ... ttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacacgagcatctaaatggaactcaatttcatgtgttgactctttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGAGCAGCACGCCAGTGGTCGACGGGGGGTTGTTCCATCATAATCATATTAC
                                   tgttgac  putative branch site (score: 3)
                                         ctctttgttt  CT-rich tract
           atctaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actattagtggcttcgtgatataccaatatgtgacaaaatagttgatgacacgagcatctaaatggaactcaatttcatgtgttgactctttgtttacagTCATCGAGAGGATGGTGACAATGGCAAGCCTGATATCAGGTTGGTTGGTGAGCAGCACGCCAGTGGTCGACGGGGGGTTGTTCCATCATAATCATATTAC

- - - - - - - - - - - - - - - - gacaaaa
- - - - - - - - - - - - - - - - - - - - -gttgatg
- - - - - - - - - - - - - - - - - - - - - - - - -cacgagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttg