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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGTCGTCGGAGGCGCCGCCGTGATGTCGCACTTTGGAAGGACGGGTCCGCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgagacctaaccctagcccccgcccccttccctctgtctctaaccgcttccttctcatattcgtcttcaccctctgctcag

Basic information

species Zea mays
transcript GRMZM2G110143_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110143_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g37960.2 (Oryza sativa), 5'ss of exon 1
-GCCGTCGTCGGAGGCGCCGCCGTGATGTCGCACTTTGGAAGGACGGGTCCGCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgagacctaaccctagccc---ccgcccccttccctctgtctctaaccgcttccttctcatattcgtcttcaccctctgctcag------
 || |  | ||| ||   |  ||  ||||||||||| || ||| |||| ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| |  |||| |||||||      ||| ||  || ||   || ||  || |  |||||| ||   ||| | | ||  || |          
GGCGGCGGGCGGGGGTTTC-TCGCCATGTCGCACTTCGGGAGGTCGGGGCCGCCGGACATCCGCGACACCTTCTCGCTCCTCGTCCTCAACATCAGCTTCCgtgagcaaaccctagccctagcgggaatcgctccgctcgctagctcgctcgcc-ccaccttctaatcggcgtttccgccgccttcctcctcgcag
















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|211438564|gb|FL360647.1|FL360647
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGGCAAGGGT
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGG-CAAGG-T
EST: gi|89757947|gb|DY687314.1|DY687314
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|149005364|gb|EE039916.2|EE039916
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|149107293|gb|EE189175.2|EE189175
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|4152004|gb|AI372138.1|AI372138
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211362372|gb|FL342933.1|FL342933
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|76290040|gb|DV029608.1|DV029608
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211277772|gb|FL330870.1|FL330870
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211470092|gb|FL331953.1|FL331953
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|50335677|gb|CO530803.1|CO530803
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211008119|gb|FL365557.1|FL365557
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|78076983|gb|DV505417.1|DV505417
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|50325433|gb|CO520559.1|CO520559
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|74243434|gb|DT651348.1|DT651348
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211347504|gb|FL349161.1|FL349161
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|89756357|gb|DY686407.1|DY686407
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|74237054|gb|DT644968.1|DT644968
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211440857|gb|FL253846.1|FL253846
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|71420359|gb|DR805069.1|DR805069
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|71321797|gb|DR797591.1|DR797591
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211235451|gb|FL353173.1|FL353173
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCYTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|31558121|gb|CD527333.1|CD527333
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|211208282|gb|FL335694.1|FL335694
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCCTCTTCGAGCGCTGCGGCAAGGTC
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCG-CTCTTCGAGCGCTGCGGCAAGGTC
EST: gi|211161811|gb|FL316356.1|FL316356
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|74241218|gb|DT649132.1|DT649132
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|30307256|gb|CD001929.1|CD001929
EST:     GGACATCCGCGACACCTTCTCGCTTGGCCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GGACATCCGCGACACCTTCTCGC-T-G-CTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|78105340|gb|DV523758.1|DV523758
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|50328942|gb|CO524068.1|CO524068
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|149101748|gb|EE287365.2|EE287365
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|71325769|gb|DR799565.1|DR799565
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
EST: gi|50328977|gb|CO524103.1|CO524103
EST:     GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCC                         GAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG
genomic: GCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgaga ... ctctgctcagGAACCACGGCCGACGACCTTTTCCCGCTCTTCGAGCGCTGCGGCAAGGTCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCGTCGTCGGAGGCGCCGCCGTGATGTCGCACTTTGGAAGGACGGGTCCGCCGGACATCCGCGACACCTTCTCGCTGCTCGTCCTCAACATCAGCTTCCgtgagcgagacctaaccctagcccccgcccccttccctctgtctctaaccgcttccttctcatattcgtcttcaccctctgctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT