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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtctacaaattttagaattattgaataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG

Basic information

species Zea mays
transcript GRMZM2G064023_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 11
gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtctacaaattttagaattattgaataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG
                   | ||||   || | ||| || | ||      |  | |  |  | | | ||||||     |||| || ||      |  |||     ||||||    |||   | ||||| ||||| || |||||||| |||||| | |||| | |||| ||| | ||||||||||| |||||||| |||||||||||||| |||||||| || |||||||| |||
------------------gtagcttt--ttatcaattcattcaccatcttta-cttaccaggcaatctgtaaa-----aattttcaac------tgcaatagc--aataatgccgtttt-ctggttctctgaagGATATTCAAGGGAGGGAAAACTATAGCAGCTGATAATGCACTGGATTATGCAGCAAATTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTTGAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 11
gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtc-tacaaattttagaattattg-aataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG
                                    | |  |  |           ||  | |  | | ||   |  |     || |  |||||||  || |     | |||   |||||   | ||||  ||||| || ||||||| ||||||| | |||| | |||| ||| | ||||| ||||| ||||| || |||||||||||||| |||||||| || |||||||| |||
------------------------------------gtagctttttttaccaatg-catccaacatctttactttccaggcaatcctgtaaattttgtaactgcaatagtaaccctatttt-ctggttcactgaagGATCTTCAAGGATGGGAAAACTATAGCAGCTGATAATGCACTGGACTATGCAGCAAACTTTTCACACATGCTTGGGTTTGATGATCCCAAAATGCTCGAG
















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|76287895|gb|DV027463.1|DV027463
EST:     TTAAACATGATTGCTCGGCTTTCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
EST: gi|71450120|gb|DR831170.1|DR831170
EST:     TAAACATGATTGCTCGGCTTCCCAC-AGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACCATTCTCTGGATTATG
genomic: TAAACATGATTGCTCGGCTTCC-ACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATG
EST: gi|31361054|gb|CD445411.1|CD445411
EST:     TTAAACTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
EST: gi|213174510|gb|FM184748.1|FM184748
EST:     TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
EST: gi|149082725|gb|EE171943.2|EE171943
EST:     TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTTCA-GGGTGGGAAATCAATAGAAACTGACAATTCTCTGGGAT-AT
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTT-CAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGG-ATTAT
EST: gi|32859373|gb|CD999054.1|CD999054
EST:     TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
EST: gi|5915419|gb|AW053060.1|AW053060
EST:     TTAAACTTGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAG                         AATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC
genomic: TTAAACATGATTGCTCGGCTTCCACCAGTGGCTTCTTATGTTTACCGGAGgtagcttttg ... ttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtctacaaattttagaattattgaataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG
                                    tttcatttgttcttt  CT-rich tract
      tacaaattttagaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttttgttcagacatttgcttcaatttttaatgcaattactggaggtggcatcactcgaattttgtaaagttaaaattgtctacaaattttagaattattgaataatattatttcatttgttctttgaagAATTTTCAAGGGTGGGAAATCAATAGAAACTGACAATTCTCTGGATTATGCGGCAAATTTCTCACACATGCTTGGTTTTGATGACCCTAAAATGCTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA