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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactttattctggaatcctggatgtccttcgcttatggttgtgctatttttggttccatattttacacattcttattatcatctctataatctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATCCAGAAGCAAACAGGCCATTTTATGGTCCAAATCAGTGGCCTTCTAAAG

Basic information

species Zea mays
transcript GRMZM2G147882_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 2
cactttattctggaatcctggatgtccttcgcttatggttgtgctatttt-tggttccatattttacacatt-cttattat-catctctataatctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATCCAGAAGCAAACAGGCCATTTTATGGTCCAAATCAGTGGCCTTCTAAAG
     ||  | |    | ||  |   | ||  ||    || | |  || | | |||     |  | ||  || | || ||| |||   | |   |  |||||||||||||||||||||| |||||||| ||  ||||| |||| | |||||||||| |||||||||| ||||| |||||||||||||||||||| ||  | |
-tgcatagacagctgccttgagtaaacctcatttcattttctacagttatgtagtttttcctgctccaggtttcatactattcatacttgtg--cattttcagGTGACTACAAGGAAGGGTATTATATAGGTATTGAGATACCAGAAGATGATCCACAAGCAAACAGACCATTCTATGGTCCAAATCAGTGGCCATCCGATG
















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|211501569|gb|FL375241.1|FL375241
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|32858736|gb|CD998417.1|CD998417
EST:     TACCACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: TA-CACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|88756322|gb|DY540463.1|DY540463
EST:     GTACACACCCATGCTAGATGATATTCTTGATCCTGAGAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGCAGTTGAGGTACCTGCTGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|74241070|gb|DT648984.1|DT648984
EST:     ACACACCCATGCTAGATGAAATTCCTTGATCCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: ACACACCCATGCTAGATGAAATTC-TTGATCC-TGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|78078284|gb|DV506699.1|DV506699
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|88756286|gb|DY540427.1|DY540427
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|93014970|gb|EB640490.1|EB640490
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|33466889|gb|CF243938.1|CF243938
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGC
EST: gi|71299023|gb|DR785502.1|DR785502
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|71429426|gb|DR810476.1|DR810476
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|50323931|gb|CO519057.1|CO519057
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATG                         GTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATC
EST: gi|211382338|gb|FL400551.1|FL400551
EST:     GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTGAATG                         GTGACTACAAGGAAGGATATTATATCGGAGTTGAGGTACCTGCA
genomic: GTACACACCCATGCTAGATGAAATTCTTGATCCTGAAAATCAAGTTAATGgtaagttatt ... tctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttggttccatattttacacattcttattatcatctctataatctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATCCAGAAGCAAACAGGCCATTTTATGGTCCAAATCAGTGGCCTTCTAAAG
                                             tctgtttc  CT-rich tract
            atattttacacattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactttattctggaatcctggatgtccttcgcttatggttgtgctatttttggttccatattttacacattcttattatcatctctataatctgtttcagGTGACTACAAGGAAGGATATTATATTGGAGTTGAGGTACCTGCAGATGATCCAGAAGCAAACAGGCCATTTTATGGTCCAAATCAGTGGCCTTCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA