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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGAGCTTGTTGTGAAGCAAGCCTTCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatctgttgaccgtgaactatgctttgtagtttgcatttcatccattctgtgtgacatcatcaatggttgtgtag

Basic information

species Zea mays
transcript GRMZM5G813143_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g28320.4 (Oryza sativa), 5'ss of exon 3
TCGAGCTTGTTGTGAAGCAAGCCTTCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatctg------ttgaccgtgaactatgctttgtagtttgcatttcatccattctgtgtgacatcatcaatggtt--gtgtag
    || || ||||||||||||||| |||||||||||  ||||||||||||| | ||||| || ||||||||||| |||||||| || ||||||||||||||||||||  |      |         ||  ||   | ||  ||| ||  | |  | | ||  |||| |||||| |||     |||||
----GCATGCTGTGAAGCAAGCCTTGAGCGCCTTGCTGTTGACTACATTGATCTGTACTATCAGCATCGCATTGACCAGTCAGTACCCATAGAGGAAACTGTGTgtatgagaacatttcttttacagaccttgtgctttaccttgaatcccttaaactttgactgacttcatcagtgggaaaatgtag

upper sequence: GRMZM5G813143_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 5'ss of exon 3
TCGAGCTTGTTGTGAAGCAAGCCTTCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatctg------ttgaccgtgaactatgctttgtagtttgcatttcatccattctgtgtgacatcatcaatggtt--gtgtag
 || || || ||||||||||||||| |||||||||||  ||||||||||||| | ||||| || ||||||||||| |||||||| || ||||||||||||||||||||  |      |         ||  ||   | ||  ||| ||  | |  | | ||  |||| |||||| |||     |||||
GCGTGCATGCTGTGAAGCAAGCCTTGAGCGCCTTGCTGTTGACTACATTGATCTGTACTATCAGCATCGCATTGACCAGTCAGTACCCATAGAGGAAACTgtgtgtatgagaacatttcttttacagaccttgtgctttaccttgaatcccttaaactttgactgacttcatcagtgggaaaatgtag
















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|78114483|gb|DV532872.1|DV532872
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|74244513|gb|DT652427.1|DT652427
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|37421025|gb|CF648209.1|CF648209
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|88756482|gb|DY540623.1|DY540623
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|91873437|gb|EB403394.1|EB403394
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|89755225|gb|DY685734.1|DY685734
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|78112032|gb|DV530428.1|DV530428
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|88757821|gb|DY541962.1|DY541962
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|76021184|gb|DT948354.1|DT948354
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|78085303|gb|DV513696.1|DV513696
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|76288052|gb|DV027620.1|DV027620
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|91055988|gb|EB166406.1|EB166406
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|211358031|gb|FL393768.1|FL393768
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAG
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAG
EST: gi|88747189|gb|DY531330.1|DY531330
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAAAAGTTGGTTGAAGAAGGAAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|91877299|gb|EB407256.1|EB407256
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|74244046|gb|DT651960.1|DT651960
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|89762828|gb|DY690268.1|DY690268
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|211368675|gb|FL393825.1|FL393825
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|89761102|gb|DY689251.1|DY689251
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|78087084|gb|DV515477.1|DV515477
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|101392434|gb|EB818146.1|EB818146
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|60396606|gb|DN229475.1|DN229475
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|91875443|gb|EB405400.1|EB405400
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
EST: gi|211437107|gb|FL416888.1|FL416888
EST:     ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACT                         ATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC
genomic: ATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatct ... ggttgtgtagATGGGAGAGCTCAAGAAGTTGGTTGAAGAAGGGAAAGTGAGGTATGTTGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGAGCTTGTTGTGAAGCAAGCCTTCAGCGCCTTGCTACTGACTACATTGATATATACTACCAACATCGCATTGATCAGTCAGTGCCTATAGAGGAAACTgtgtgtatctgttgaccgtgaactatgctttgtagtttgcatttcatccattctgtgtgacatcatcaatggttgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA