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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtcaaattatacgttttttccctcgactgtcaggctggagtggtcagtccgtgatccctttctctgtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCCGCTTTACCTGGAGAAGGTGGCATGGGCACTCACCCACAACAATCCCAAT

Basic information

species Zea mays
transcript GRMZM2G573867_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 1
gtagtcaaattatacgttttttccctcgactgtcaggctggagtggtcagtccgtgatccct-ttctctgtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCCGCTTTACCTGGAGAAGGTGGCATGGGCACTCACCCACAACAATCCCAAT
            ||  |||||| |      |       ||| | | ||| | ||||||||   | |  |   ||||||||||||||||||| ||||||||| |||||||||||||||| |||||||||||||| ||||||||||||||| | ||||||||||| |||||||| || |||
-----------gtattttttttgctggatttagtgaattggtgcgatcatttcgtgatcctgatgccttagctgcgcagGCATGTTCATGGGAAGAGGGTTTTGGTGGTGACCAACACCACCGTCGCGCCGCTCTACCTGGAGAAGGTGACCTGGGCACTCACGCACAACAACCCGAAT
















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|148956744|gb|EC902625.2|EC902625
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|50329036|gb|CO524162.1|CO524162
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|148946595|gb|EC891854.2|EC891854
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|50336564|gb|CO531690.1|CO531690
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|88746263|gb|DY530404.1|DY530404
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGAAGAGCCAGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGAGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|78082241|gb|DV510653.1|DV510653
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|88746349|gb|DY530490.1|DY530490
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGAAGAGCCAGACTTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
EST: gi|149043950|gb|EE047432.2|EE047432
EST:     CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAG                         GCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC
genomic: CCGATCTACATCGGCGCAGGCCTCCTCGACGAGCCGGACCTGCTGCAGAGgtagtcaaat ... gtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcgactgtcaggctggagtggtcagtccgtgatccctttctctgtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCCGCTTTACCTGGAGAAGGTGGCATGGGCACTCACCCACAACAATCCCAAT
                                  tccctttctctgtttg  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtcaaattatacgttttttccctcgactgtcaggctggagtggtcagtccgtgatccctttctctgtttgcgcagGCATGTTCATGGTAAGAGGGTTCTGGTGGTGACCAACACGACCGTCGCGCCGCTTTACCTGGAGAAGGTGGCATGGGCACTCACCCACAACAATCCCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA