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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG

Basic information

species Zea mays
transcript GRMZM2G005849_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005849_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os12g03720.1 (Oryza sativa), 3'ss of exon 9
gtaatga---taaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG
||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   ||||||||||||||||| ||||| ||||| || |||||||| || |||| |||||| ||||||||||||||||| | |||||| ||  | || || |||||||| ||    
gtaagcgctttggacagactgcagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCAGTTTGCCCTAGTGGATCT

upper sequence: GRMZM2G005849_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os11g03900.1 (Oryza sativa), 3'ss of exon 9
gtaatga---taaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG
||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||||||||||| || ||||| || |||||||| || |||| |||||| ||||||||||||||||| | |||||| ||  | || || |||||||| ||    
gtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT
















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|211507116|gb|FK960930.1|FK960930
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|7216484|gb|AW562606.1|AW562606
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|89248870|gb|DY620656.1|DY620656
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|211507111|gb|FK960925.1|FK960925
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCG
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCG
EST: gi|148955139|gb|EC900656.2|EC900656
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|71771453|gb|DR969390.1|DR969390
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|149005283|gb|EE039832.2|EE039832
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|47962136|gb|CN844845.1|CN844845
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTC
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTC
EST: gi|211029256|gb|FL478423.1|FL478423
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACTCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAGCAGCTCCTCTCGCGTAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|149014771|gb|EE044463.2|EE044463
EST:     GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: GACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
EST: gi|111197488|gb|EE295623.1|EE295623
EST:     CCGAGAACCTCCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAG                         CAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT
genomic: ACGAGAACCT-CCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaatgataa ... cctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG
                                             cctcttgc  CT-rich tract
                                    ttttcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcagCAAGCAGCAGTCGGTGATCCAACAGCTCCTCTCGCGCAGGGGGCGCCTGATAGTGATGTGCTCTAGGGGAGATGCCGCGGCTGTGTGCCCTAGCGGTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG