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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtatttatctccactattttctcctggtgttgttaaactgggatgactattatcttatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcag

Basic information

species Zea mays
transcript GRMZM2G413857_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G413857_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g09670.1 (Oryza sativa), 5'ss of exon 8
GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagta-tttatctccactattttctcctggtgttgttaaactgggatgactattatcttatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcag
|| |||||||| || || ||||| ||||| ||||||||||| |||||||| |||||||| |||| || |||||| |       | ||| | |  ||    ||  | || |  || ||  ||| ||  | |||  |    | |   || ||  |||  | | ||| | |||||
GAAGTTCGTGGGAATGGACAAGACCCTGAATCAGAGATTGTGCAAGCCTGTAGAAGTgtaagtagttcatctcctcgtcagctttctgatatgatt---ttgacaagattggtagct-gtctacttatagaaagtt---agtctgaagca--ataggtttccttttatgcag
















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|22491529|gb|BU051452.1|BU051452
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGG
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGG
EST: gi|32804882|gb|CD957118.1|CD957118
EST:     GATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|19351457|gb|BM895989.1|BM895989
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAATGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|87152801|gb|DY397590.1|DY397590
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAATGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
EST: gi|67023933|gb|CO452682.1|CO452682
EST:     GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGT                         TTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT
genomic: GTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtattt ... ttctgtgcagTTACTTGACGAGAGGCAGGGAGCTAACGTCTGGCGGTTCCTTCAGGCAATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGTTCGTGGTAACGGGCAAGATCCTGAGTCAGAGATTGTCCAAGCCTGCAGAAGTgttagtatttatctccactattttctcctggtgttgttaaactgggatgactattatcttatctgctacttgaacatgtaaaattaaaaacatgataaatcttcttctgtgcag

- - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT