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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtcctgcgatttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG

Basic information

species Zea mays
transcript GRMZM2G054247_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g50360.1 (Oryza sativa), 3'ss of exon 1
------------gtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtcctgcgatttggtttc------agGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG
              |     ||| || ||| ||||   | ||   ||  |   ||  || || |      || ||||| ||||  ||  ||||  |||       ||||| || ||||||||||||||| |||||||||| |||||||||||||||||||||||||||
gtcagtaaaacccgctccaaatctccatttgtttttcct-tcttctttttccgagggaggagattgttaatg-tgatttgggttttgacattttttttttgggttagGTCGGACGGGGCGCAGCCGCACTTGGTGAACATTCAGTTCCAGAAGAAGGTGCAGCTGCAG

upper sequence: GRMZM2G054247_T03 (Zea mays), 3'ss of exon 1
lower sequence: EFJ26697 (Selaginella moellendorffii), 3'ss of exon 1
gtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtc-ctgcgatttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG---------------------------------------
                           || |   || |     || |    |     |    |  || | || ||| | ||     | || || ||||| |||||||||||  ||||||||||||||||||||||||||||||   |||||                                       
---------------------------gtaggggtattgtgttcttgcgcatt---ttccccgtctctgatcgctggggtt----cttagATCCGATGGCGCGCAGCCGCATTTGGTGAACATCCAGTTCCAGAAGAAGGTGCGCTTGCAGCTGCTGGCGATTTACGTGGATTTCAAGCTGGATGAGAGC
















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:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|89252141|gb|DY623927.1|DY623927
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|76915292|gb|DV165923.1|DV165923
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|60400666|gb|DN233473.1|DN233473
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|74244865|gb|DT652779.1|DT652779
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCG
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCG
EST: gi|211282122|gb|FL372019.1|FL372019
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAAC-TCGACACCTACTGGCA                         GTCTGATGGGGCGCAGC
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGC
EST: gi|211201873|gb|FL396465.1|FL396465
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACNACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|78088159|gb|DV516552.1|DV516552
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|13515650|gb|BG517926.1|BG517926
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|22490544|gb|BU050467.1|BU050467
EST:     CGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: CGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71297609|gb|DR784753.1|DR784753
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|12045796|gb|BF727935.1|BF727935
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71422983|gb|DR805911.1|DR805911
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|78180912|gb|DV551285.1|DV551285
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|211341306|gb|FL394252.1|FL394252
EST:     GGCAACGGCGTCGCGGCC-TGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGC
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGC
EST: gi|71297610|gb|DR784754.1|DR784754
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71427966|gb|DR809016.1|DR809016
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|149073064|gb|EE161334.2|EE161334
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|211368075|gb|FL362342.1|FL362342
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAATAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
EST: gi|71449488|gb|DR830538.1|DR830538
EST:     GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCA                         GTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT
genomic: GGCAACGGCGTCGCGGCCCTGCGCGACGACAACCTCGACACCTACTGGCAgtcagtggat ... ttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtggatcacctttttttttctttgtcgaattagttgaagctagaaggtcagagttggtgattcgggtcctgcgatttggtttcagGTCTGATGGGGCGCAGCCGCACCTGGTGAACATCCAGTTCCAGAAGAAGGTGCAGCTGCAG

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