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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcagagtctgcttattttattaaggcttactggtattacatatgcagaacatataattagctgatgtatagtaactgatagcatctattcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTGATCAAACAAAACAGCAGGGTTATATTGCCTATCATCTTTCCTGCACTGG

Basic information

species Zea mays
transcript GRMZM2G369912_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G369912_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g62730.3 (Oryza sativa), 3'ss of exon 3
catcagagtctgcttattttattaaggcttactggtattacatatgcagaacatata-attagctgatgtatagtaactgatagcatctattcttgttc-agGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTGATCAAACAAAACAGCAGGGTTATATTGCCTATCATCTTTCCTGCACTGG
     |    || | ||   | | |   | |   | |  | | |      | |   | ||| | ||||| ||  || || ||||    ||| ||  ||| ||||||||||| | ||  | ||||||||||| || || || ||||||| ||||||||||||||| || ||||| || || ||||||||||| |||||||| |
tgcggggaattgttaatgcaaattatattga--agcagcagaaacatgatatacgcatattggttgatggattttatctaatagtgcttatgctacttctagGTTGCTGAGAGAGCATTGTTTTTGTGGAACAATGATCATATCGAGAATCTGATCAAACAAAATAGTAGGGTGATCTTACCTATCATCTTCCCTGCACTCG
















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|33095312|gb|CF055306.1|CF055306
EST:     CACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: CACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|18660996|gb|BM501157.1|BM501157
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|211511805|gb|FL413831.1|FL413831
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTA
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTA
EST: gi|211182071|gb|FL377604.1|FL377604
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|148965285|gb|EE016089.2|EE016089
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|211133221|gb|FL428361.1|FL428361
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|87157382|gb|DY402171.1|DY402171
EST:     CCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: CCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|26457005|gb|CA828588.1|CA828588
EST:     CCTCTCTTCCGCCAGATCGCACGTTTTCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: CCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|22935403|gb|BU571678.1|BU571678
EST:     TGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|26560104|gb|CA832339.1|CA832339
EST:     CCTCTCTTCCGCCAGATCGCACGCTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: CCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
EST: gi|213172114|gb|FM190146.1|FM190146
EST:     TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAG                         GTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG
genomic: TCCCTCTCTTCCGCCAGATCGCACGTTGCCTGAATAGCTCACACTTTCAGgtaatggttg ... tcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcagaacatataattagctgatgtatagtaactgatagcatctattcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTGATCAAACAAAACAGCAGGGTTATATTGCCTATCATCTTTCCTGCACTGG
                                        tctattctt  CT-rich tract
     acatataatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catcagagtctgcttattttattaaggcttactggtattacatatgcagaacatataattagctgatgtatagtaactgatagcatctattcttgttcagGTTGCTGAGCGGGCGCTATTTTTGTGGAATAACGACCACATCGAGAGTCTGATCAAACAAAACAGCAGGGTTATATTGCCTATCATCTTTCCTGCACTGG

- - - - -ctgctta
- - - - - - - - - - - - - - -tactggt
- - - - - - - - - - - - - - - - - - - - catatgc
- - - - - - - - - - - - - - - - - - - - - - - - gaacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg