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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattag

Basic information

species Zea mays
transcript GRMZM2G143462_T04
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G143462_T06 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g08300.2 (Oryza sativa), 5'ss of exon 6
AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatt-tttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattag
 ||||| |||||||| ||||||||||||| ||||||||||||||| ||||| ||||| ||||| |||||||| || |||||||||||||| || || |||||||||  | ||||    ||      | | ||    ||||     ||| | |   |   ||| ||               | ||| |  ||||||||||
GATGGAAATGGGTGGTGGCAGTTGGGACAGAGATAAAGTCCAAAGAGCTCTACGTGCAGCTTATAACAACCCAGAGCGTGCTGTTGAATATCTATATTCTgtatgttctgtttcctcctgtaaatgtttgttattcttttttttctaacgttaatagataatgtt---------------tgtttctcccaaacattag
















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|211394218|gb|FL229512.1|FL229512
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGSTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|149095756|gb|EE181396.2|EE181396
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|148995692|gb|EE034914.2|EE034914
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTG
EST: gi|89759371|gb|DY688230.1|DY688230
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCCATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|74242202|gb|DT650116.1|DT650116
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|148947026|gb|EC892323.2|EC892323
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGGTGGTCAAGGGGC
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGG-TGGTCAAGGGGC
EST: gi|89758471|gb|DY687642.1|DY687642
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|89761592|gb|DY689541.1|DY689541
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTTCCA-TTGGTGGTCAAGG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTT-CCAATTGGTGGTCAAGG
EST: gi|211394220|gb|FL229514.1|FL229514
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|211488314|gb|FK957004.1|FK957004
EST:     TCCGTGCCGCTTACAACA-CCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTNGAATTTGCTGTCCCANTTGGTGGTCAAGGGGC
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCT-GAAATTGCTGTTCCAATTGGTGGTCAAGGGGC
EST: gi|78111156|gb|DV529553.1|DV529553
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         --TA----A----CAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|148999208|gb|EE036127.2|EE036127
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGTGGTCAAGGGGCA
EST: gi|93280956|gb|EB673220.1|EB673220
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTTCCA-TTGGTGGGTCA-GGGG
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTT-CCAATTGGTGG-TCAAGGGG
EST: gi|76912415|gb|DV164721.1|DV164721
EST:     TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCT                         GGTATTCCAGTAACAGCTGAAATTGCTGTTCCNATTGGT
genomic: TCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtattt ... caaacattagGGTATTCCAGTAACAGCTGAAATTGCTGTTCCAATTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAGATGGGTGGGGGCAGTTGGGACAAAGATAAAGTCCAAAGGGCTCTCCGTGCCGCTTACAACAACCCCGAACGTGCTGTTGAATACCTCTACTCTgtatgtatttttctcattgccccattcttttgcatttttgcacttaatgatggaatccaattttctggtgctaatagattatttatgtcaaacattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT