Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtag

Basic information

species Zea mays
transcript GRMZM2G054247_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 5'ss of exon 2
GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgcttcagtagagat-gctactcctttgccttgt--gattcga-tggtt--ttgagactaattggttcta------tgttgtgcggtag
||| || ||||||||||||||| |||||||||| ||||||||||||||||||||||||||||||  ||     | |    |  ||    ||     ||||  ||||||| ||| |  | | |  || ||| | ||       ||||| |  | ||
GTCGGACGGGGCGCAGCCGCACTTGGTGAACATTCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgagtggagagggattcctcacttgggctcaattttgtttgattcgagtggataatcgtgcttagttgttcctcccttgctgttgcgtcgcag
















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|91873254|gb|EB403211.1|EB403211
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|89252141|gb|DY623927.1|DY623927
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGA
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGA
EST: gi|76915292|gb|DV165923.1|DV165923
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|60400666|gb|DN233473.1|DN233473
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|78088159|gb|DV516552.1|DV516552
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|13515650|gb|BG517926.1|BG517926
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71297609|gb|DR784753.1|DR784753
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|12045796|gb|BF727935.1|BF727935
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71422983|gb|DR805911.1|DR805911
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|78180912|gb|DV551285.1|DV551285
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71297610|gb|DR784754.1|DR784754
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCTG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71427966|gb|DR809016.1|DR809016
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|87153735|gb|DY398524.1|DY398524
EST:     CGCAGCCGCACNTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|149073064|gb|EE161334.2|EE161334
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71427965|gb|DR809015.1|DR809015
EST:     CCTGGTGAACATCCATTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTTTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|211368075|gb|FL362342.1|FL362342
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAATAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|94476642|gb|EB705600.1|EB705600
EST:     CCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
EST: gi|71449488|gb|DR830538.1|DR830538
EST:     CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG                         CTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC
genomic: CGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgctt ... tgtgcggtagCTCGTTGTGCTCTACGTGGATTTCAAGCTCGACGAGAGTTACACGCCGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAGgtgcctgcttcagtagagatgctactcctttgccttgtgattcgatggttttgagactaattggttctatgttgtgcggtag

- - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG