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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaattcgtaagcctttgttgcagttatgcttatttaatcaaggagaagttaacttaattcatcttcttatcccttttatcttgatggtggttttgggttcag

Basic information

species Zea mays
transcript GRMZM2G006468_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006468_T05 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os08g26870.4 (Oryza sativa), 5'ss of exon 5
GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaattcgtaagcctttgttgcagttatgcttattt--aatcaaggagaagttaact--taattcatcttcttatcccttttatcttgatggt-ggttttgggttcag
||| |||||||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||  |||  | | ||   | | | | |||| || ||  ||  ||  |||   || |  ||   | |||||| |  |||| ||||  ||| |  || | | |||||| | |||
GCAAGACCAACCATATATCAAGTTGTGAAGGAGATGATTGATAAGATGGGTTATGAGgtaaggtta-ctagaaatagtctatagtagttgtgtttggttacaaataagtcaaattgtaccactcattcatttatttattccttccatcattgtgtttgattttggttccag
















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|60399773|gb|DN232583.1|DN232583
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|14244855|gb|BG842793.2|BG842793
EST:     TAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: TAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|16925921|gb|BM078989.1|BM078989
EST:     NACCATATATCAAGTTGTCAAGGAAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: -ACCATATATCAAGTTGTCAAGG-AAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|76010925|gb|DT938095.1|DT938095
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|5895762|gb|AW037008.1|AW037008
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|14243138|gb|BG840841.2|BG840841
EST:     TATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: TATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|14242681|gb|BG840373.2|BG840373
EST:     AACCATATATCAAGTTGTCAAGGAAATGATTGANTAAA-TGGGCTATGAG                         GTAAAACTTGTTCGGGTAAA
genomic: AACCATATATCAAGTTGTCAAGGAAATGATTGA-TAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAA
EST: gi|211436012|gb|FL361903.1|FL361903
EST:     CAACCATATATCAAGTTGTCAAGGAAATGAATGATAAATTGGGCTATGAG                         GTAAAACTTGTTCGGGTAAAC
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAAC
EST: gi|211186703|gb|FL252848.1|FL252848
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAA
EST: gi|13178078|gb|BG349336.1|BG349336
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|211186706|gb|FL252851.1|FL252851
EST:     AAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: AAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|71774336|gb|DR972214.1|DR972214
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|60346391|gb|DN213364.1|DN213364
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|89755425|gb|DY685846.1|DY685846
EST:     AAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: AAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|76010926|gb|DT938096.1|DT938096
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|60355084|gb|DN222057.1|DN222057
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|211436290|gb|FL481825.1|FL481825
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|74242180|gb|DT650094.1|DT650094
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|60358728|gb|DN225701.1|DN225701
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|13178561|gb|BG349819.1|BG349819
EST:     ATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: ATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|13177698|gb|BG349129.1|BG349129
EST:     AAATGGGCTATGAG                         GT-AAACTTGTTCGGGT-AGCAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: AAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|71774337|gb|DR972215.1|DR972215
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|78113266|gb|DV531659.1|DV531659
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
EST: gi|211505179|gb|FL436188.1|FL436188
EST:     CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAG                         GTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA
genomic: CAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaa ... ttgggttcagGTAAAACTTGTTCGGGTAAACAAAAGAATTCAAGAAGCGTACTGTGCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACGACCAACCATATATCAAGTTGTCAAGGAAATGATTGATAAAATGGGCTATGAGgtaatcttaattcgtaagcctttgttgcagttatgcttatttaatcaaggagaagttaacttaattcatcttcttatcccttttatcttgatggtggttttgggttcag

- - - - - - - - - - - - -  AAGGAA