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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccagctgccgctggacggaagcatatatctggctggtgataatgctctgaactaactgatctcagtggcggcggggtgttctcgccttgtcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA

Basic information

species Zea mays
transcript GRMZM2G147882_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 3'ss of exon 9
---------------tccagctgccgctggacggaagcatatatctggctggtgataatg-----ctctgaa------ctaactgatctcagtggcggcgg--ggtgttctcgccttgtcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA
               | ||     |     ||   |  |  || || | |   |    ||     ||||  |        || | |    | ||||         |  | |  |  |   |  ||||||| || | ||| ||||||||||||||||| ||||| || ||||||||||| |||||||| || |||||||||||||||||
gtaagtttcttctcatacataaatcttcatacaagatgagctaactcgttaacggcgctgcaagcctctacaaatcttacaaataaatcgaatggctttaattactccttttccaattcttcaaacagATTGCGTTCTTTGTGGAACCAAGCCACGATTGCGTAGTCGAGTGCCTGCCAACCTGCAAATCTGAATCAAATCCTCCAAA
















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|78077655|gb|DV506089.1|DV506089
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32924156|gb|CF028968.1|CF028968
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGAC
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGAC
EST: gi|211415426|gb|FL477512.1|FL477512
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32924444|gb|CF029256.1|CF029256
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|211525267|gb|FL432922.1|FL432922
EST:     GTCCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GT-CAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923806|gb|CF028618.1|CF028618
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCCCGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32924110|gb|CF028922.1|CF028922
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGG
EST: gi|71299018|gb|DR785501.1|DR785501
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCTTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923874|gb|CF028686.1|CF028686
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32924334|gb|CF029146.1|CF029146
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923638|gb|CF028450.1|CF028450
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|76287314|gb|DV026882.1|DV026882
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|71429425|gb|DR810475.1|DR810475
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32858735|gb|CD998416.1|CD998416
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923912|gb|CF028724.1|CF028724
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923869|gb|CF028681.1|CF028681
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32923708|gb|CF028520.1|CF028520
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|32924079|gb|CF028891.1|CF028891
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGTTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
EST: gi|74241069|gb|DT648983.1|DT648983
EST:     GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCG                         ATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG
genomic: GTCAACCTTACATCGAGTGGTCCTAGATGGGCGAGAACGCTACTCGgtaagtttcg ... tcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgaactaactgatctcagtggcggcggggtgttctcgccttgtcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA
                                  ttctcgccttgtctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccagctgccgctggacggaagcatatatctggctggtgataatgctctgaactaactgatctcagtggcggcggggtgttctcgccttgtcttgaacagATAGCCTACTTCGTGGAACCAAGCCACGACTGCGTGGTGGAGTGCCTGCCGACCTGCAAGTCCGAATCAAATCCTCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG