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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtgctcagtagtcatttgtgtccattgccgctctgctttgtgctcgctctgtttgtttgttgtcgactccattgacggccgctgatacttacatggttgatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGGTGAACTACATGAAGACCCGACTTGGCCAGGTGAACTCCGTTGCCTCCAA

Basic information

species Zea mays
transcript GRMZM2G020484_T08
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020484_T08 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g04950.2 (Oryza sativa), 3'ss of exon 1
gtcagtgctcagtagtcatttgtgtccattgccgctctgctttgtgctcgctctgtttgtttgttgtcgactccattgacggccgctgatacttacatggttgatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGGTGAACTACATGAAGACCCGACTTGGCCAGGTGAACTCCGTTGCCTCCAA
|| |||   ||  | || |    ||| ||||||   ||  || ||   |  |  | | ||  | | |   |   | |||  |   |||||  || ||   | | | | ||||| ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||||||||| || || || |||| || | || ||||| ||||
gtaagtaa-caaca-tcttcctcgtcgattgccaagcttgttcgtctccatt--gatggtgagatataagcg--agtga-agtgactgatgtttgca--atggtttgatcagCTAACGAGTGCTGCGAGAGGCTGGCCTACTATGGCATGAGCACCAACCTCGTGAACTACATGAAGACGCGGCTCGGGCAGGAGAGCGCCATTGCCGCCAA
















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|211365735|gb|FL263996.1|FL263996
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|148974530|gb|EE025317.2|EE025317
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|149106098|gb|EE291762.2|EE291762
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|149099731|gb|EE185781.2|EE185781
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|89760037|gb|DY688639.1|DY688639
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|148972810|gb|EE023795.2|EE023795
EST:     CGACGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|78112564|gb|DV530958.1|DV530958
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|74234545|gb|DT642459.1|DT642459
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|76936415|gb|DV174717.1|DV174717
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|149101742|gb|EE287361.2|EE287361
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|101394497|gb|EB819183.1|EB819183
EST:     CTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|149074406|gb|EE162795.2|EE162795
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|50323834|gb|CO518960.1|CO518960
EST:     CGCCGTGAAGAAGGGCACCGGTAACTGGCGCGCCTGCCCCTACATCCTCT                         CTAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|71439086|gb|DR820136.1|DR820136
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|76925417|gb|DV170443.1|DV170443
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
EST: gi|148949850|gb|EC895341.2|EC895341
EST:     CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCG                         CGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG
genomic: CGCCGTGAAGAAGGGCACCGGCAACTGGCGCGCCTGCCCCTACATCCTCGgtcagtgctc ... gatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgttgtcgactccattgacggccgctgatacttacatggttgatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGGTGAACTACATGAAGACCCGACTTGGCCAGGTGAACTCCGTTGCCTCCAA
                               atactta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtgctcagtagtcatttgtgtccattgccgctctgctttgtgctcgctctgtttgtttgttgtcgactccattgacggccgctgatacttacatggttgatggttcagCGAACGAGTGCTGCGAGAGGCTGGCTTACTATGGCATGAGCACCAACCTGGTGAACTACATGAAGACCCGACTTGGCCAGGTGAACTCCGTTGCCTCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA