Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaccactggatccatgtgtctcacgctataccctcgccctagatccttgcgggttgctgacccccttcagttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAG

Basic information

species Zea mays
transcript GRMZM5G862331_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862331_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g52140.2 (Oryza sativa), 3'ss of exon 1
------gtaccaccactggatccatgtgtct-cacgctat-accctcgccctagatcc--ttgcgggttgctgacccccttcagttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAG
       |||| |||   |||||  |  |||     |||| | |||  |||||  ||   | || |  | || ||||| ||  | |   |||||||||||||||||||| |||||||||| |||||||||||||||||||| || ||||| ||||||||||| |||||||||||||||||||||||||||||||
gtctccctacctccat--gatccgcgcatctatggtctatgaacctaaccctacttcgagtagctgactact-accccatttggcttgttgcagCTGCAGGAGCTCGACCAGATGAAGCGAAGGCTGAAGGAGATGGAGGAAGAGGCCGCGGCCCTCCGCGACATGCAGGCCAAGGTCGCCAAGGAGATGCAAG
















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|87152025|gb|DY396814.1|DY396814
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
EST: gi|211131812|gb|FL249254.1|FL249254
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGCGATGGAGGAGGAA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
EST: gi|9461255|gb|BE453642.1|BE453642
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCA
EST: gi|211130892|gb|FL249249.1|FL249249
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
EST: gi|211131815|gb|FL249257.1|FL249257
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
EST: gi|161594401|gb|EY963782.1|EY963782
EST:     CGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
genomic: CGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
EST: gi|18964307|gb|BM660930.1|BM660930
EST:     TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAG                         CTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA
genomic: TGGACGGCGCTGACGTTGATATGGCTGCCTCCGGGGATGACGCGGCGAAGgtaccaccac ... ttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctataccctcgccctagatccttgcgggttgctgacccccttcagttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAG
                             tgctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccaccactggatccatgtgtctcacgctataccctcgccctagatccttgcgggttgctgacccccttcagttgcgtgcagCTGCAGGAGCTCGACGAGATGAAGCGCAGGCTGAAGGAGATGGAGGAGGAAGCCGCCGCCCTCCGCGATATGCAGGCCAAGGTCGCCAAGGAGATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG