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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGCCGATAGTTCTGTTCTACTGGAGGAGGAGCAGAGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgtttgttcatccttttgatttcgcccccatgcgattcattggttctaggttcagcgttttctcgccatgtgttttcgtagggttcgacgtag...

Basic information

species Zea mays
transcript GRMZM5G862101_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862101_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 1
--GAGGCCGATAGTTCTGTTCTACTGGAGGAGGAGCAGAGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatga----------ttgtttgttcatccttttgatttcgcccccatgcgattcattggttctaggttcagcgttttctcgccatgtgttttcgtagggttcgacgtag
    ||  |  ||    ||      || || |||  || |   | ||||||||| ||||||||||||||| |||||||||| |||||||| ||||| |||||||| |           || ||  ||| || | |||||||||  | |   |||||| |||| | | || ||  || | ||         ||  |  | || |         
ATCGGGGAGGGAGAGAGGTCGAGGAGGCGGCGGA--AGGGGAGAGGATGGGGTCTGGATCTTTCCTCAAGCTGCTGGCCAACAACTTCGACGTCCTCGCCGGgtacgggcggggtttcttcttccttcctcttcttgatttcgttcgccgccgattcgttggctgt-ggctcgtcgatgtcgatttggtggtggttcttggtt---------
















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|211223200|gb|FL136732.1|FL136732
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|32858463|gb|CD998144.1|CD998144
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|14245109|gb|BG873691.1|BG873691
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223194|gb|FL136726.1|FL136726
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|71771977|gb|DR969914.1|DR969914
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223203|gb|FL136735.1|FL136735
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGNCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223202|gb|FL136734.1|FL136734
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223197|gb|FL136729.1|FL136729
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211221143|gb|FL136724.1|FL136724
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223201|gb|FL136733.1|FL136733
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223204|gb|FL136736.1|FL136736
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT
EST: gi|211223195|gb|FL136727.1|FL136727
EST:     TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGG                         GCCACTCATATCACTTGCTTATCCTCT
genomic: TCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgt ... ttcttttcagGCCACTCATATCACTTGCTTATCCTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGCCGATAGTTCTGTTCTACTGGAGGAGGAGCAGAGAGCAAGATGGGGTCCGGATCTTTCCTCAAGGTGCTGGCCAAGAACTTCGATGTCCTTGCCGGgtatgattgtttgttcatccttttgatttcgcccccatgcgattcattggttctaggttcagcgttttctcgccatgtgttttcgtagggttcgacgtag

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