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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcag

Basic information

species Zea mays
transcript GRMZM2G143602_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 4
TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcagata------tactaaaaactctcattgttggttc--------aatggctaacagca---gttaat-tcag--------------------
||||||||||||| |||||||| ||||||||  | ||||||||||| |||||||||||||| || ||||||||||||||||||||||||||||| || ||||||  ||| |||      |  |||    | |     ||| ||         | |   ||||| ||    ||||| | ||                    
TTATGATAGATCACGAGCTTCGAAAACTCCGATTAATAGACTGGGGCCTTGCTGAATTCTACCACCCTGGCAAGGAATATAATGTCCGTGTTGCTTCAAGgtaggggcacatactgctctgttaatgggtttatcatttgattttcttatagagtaattaacaacatgtattaatcttagtatgtttggtgaactattta

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 4
lower sequence: PP1S63_208V6.1 (Physcomitrella patens), 5'ss of exon 5
TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcagata--tactaaaaac----tctcattgttgg------ttcaatggctaacagcagttaattcag--------------------------
| ||||| || || ||||  || || ||  | ||||| || ||||| || ||||| |||||||| |||||||| ||||||||||| |||||||| ||||||||  | |  |    | ||     |    ||| |  |  ||      |||||    |   | ||   |||  ||                          
TAATGATTGACCACGAGCAACGAAAGCTGAGACTGATTGATTGGGGACTCGCTGAGTTCTATCACCCTGGCAAAGAATATAATGTGCGTGTTGCCTCCAGgtaagttctaaaggcttctcgtggcactgtcttaacgagggattcatttcaagaaatcgtatcatagaatgtagtggttactgtggattattattaattt

upper sequence: GRMZM2G143602_T03 (Zea mays), 5'ss of exon 4
lower sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 5
TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgt-agctgcagata-tactaaaaactctcattgttgg------ttcaatggctaacagcagttaattcag------------------------------
| ||||| || |||||||  ||||| ||  |||| || |||||||| ||||| |||||||||||||||||||| || |||||||| |||||||| || |||| || | ||||   | ||  |  |  | | |   ||      ||  ||        || |  ||| | |                              
TGATGATTGACCATGAGCAGCGGAAGCTTAGGCTTATTGACTGGGGACTTGCCGAATTCTATCATCCTGGCAAAGAGTATAATGTGCGTGTTGCCTCTAGgtgagtttcagaggcttcttgaggcagttacttagggaggactttatattatgtttggctgagaatccggacatcagaatcatgcttcatcgagtaagct

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|61117728|gb|DN558689.1|DN558689
EST:     TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|60396112|gb|DN228981.1|DN228981
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|19822196|gb|BQ048220.1|BQ048220
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|60395786|gb|DN228656.1|DN228656
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|60343609|gb|DN210582.1|DN210582
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|21389960|gb|BQ528009.1|BQ528009
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|29576768|gb|CB616880.1|CB616880
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|20507674|gb|BQ279724.1|BQ279724
EST:     TAATGTCCGTGTTGCATCCAG                         GTGCTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: TAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|60340369|gb|DN207342.1|DN207342
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|211466861|gb|FL187159.1|FL187159
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|78073838|gb|DV502272.1|DV502272
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|87156472|gb|DY401261.1|DY401261
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGNCA-GATTATGATTACT
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTG-CAAGATTATGATTACT
EST: gi|71770653|gb|DR968590.1|DR968590
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC
EST: gi|60395745|gb|DN228615.1|DN228615
EST:     GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAG                         GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTATTC
genomic: GCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcag ... gttaattcagGTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGATAGATCATGAGCTTCGGAAACTCCGGCTGATAGACTGGGGTCTTGCTGAATTCTATCATCCTGGCAAGGAATATAATGTCCGTGTTGCATCCAGgtagctgcagatatactaaaaactctcattgttggttcaatggctaacagcagttaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA