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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcattcgccagcttcgttccccactttgtgaaggttgagacgcttctgaatctttgctcgttgtgttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGC

Basic information

species Zea mays
transcript GRMZM2G540403_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 3
--------------gttggttcatt--cgccagcttcgttccccactttgtgaa--ggttgagac-gcttctgaatctttgctcgttgtgttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGC
              | || |  |||  | ||||||||  | ||   || | | |   | ||   | |||||||||||     || ||||||  |||| ||||||||||||| ||||||||||| |||||||||| |||||| |||||   ||| ||  ||||||||||||||||  | |||||||| || ||||| ||||
gttgctttcgttttgctgatcgattttcaccagcttccctgccttgttggaggattagctgtaccagcttctgaatcg--aatcattgtgt--ctgt-agGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCGGCTCTCCAGCGATCCAGGAGAGGAATCGGCGATGGATCCGTCGGGATGC
















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|149109204|gb|EE190074.2|EE190074
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATCCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|78112113|gb|DV530509.1|DV530509
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|211175056|gb|FL087597.1|FL087597
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATA
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATA
EST: gi|8367157|gb|BE050102.1|BE050102
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|211175053|gb|FL087594.1|FL087594
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACA
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACA
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|78121537|gb|DV539921.1|DV539921
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
EST: gi|211175055|gb|FL087596.1|FL087596
EST:     GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAG                         GGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG
genomic: GCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttcat ... ttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactttgtgaaggttgagacgcttctgaatctttgctcgttgtgttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGC
                            aatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttcattcgccagcttcgttccccactttgtgaaggttgagacgcttctgaatctttgctcgttgtgttactgtcagGGTGTCTACTACTACTTCTACCAAATATTCCGGAACAGGGCCGAGGCAAGGGCCCTTGAGCGATCCAGGAGAGGGCTTGGCGATGGGTCTGTCGGCATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG