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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacatccttttgtctttatatggggctcttggcctatcagtaaaaataataattcaggaaatcgacttgatcctgatatttagaataacatgtttcgtttgtattataatctgtttccag

Basic information

species Zea mays
transcript GRMZM2G096585_T05
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G096585_T05 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 5'ss of exon 7
TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAA---GAGCCATTTAAATTCAAGACCGATGAAGgtaagaacatccttttgtctttatatggggctcttggcctatcagtaaaaataataattcaggaaatcgacttgatcctgatatttag-aataacatgtttcgtttgtattataatctgtttccag
||||||| |  ||||| |||||||||||  |  | |||||||||||||||||||| |||   ||||||||| |||||||||| |||||||||  |      |   |  || |||   || |  |   | | | |||  ||| ||         | |  |   | |  ||||||  ||| || ||| |||| | |||  ||| || | |  ||||||
TCAAAATAACTGGAAAACTTCAGGATGGTACAATATTTACAAAGAAGGGGCATGATGAACCAGAGCCATTTGAATTCAAGACTGATGAAGgt--gctttgtcaacttcctctatgctgg-ccatacacttttaagttcaaacaa---------ataatgttcttactctgataagtagtaacaacttgttcccttttgatt-tactttccttccag
















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|32931241|gb|CF036053.1|CF036053
EST:     AAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: AAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211281609|gb|FL229383.1|FL229383
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211292816|gb|FL187030.1|FL187030
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211294948|gb|FL187036.1|FL187036
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|5901160|gb|AW042260.1|AW042260
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTTCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|32936507|gb|CF041326.1|CF041326
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|33094682|gb|CF054676.1|CF054676
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|71596242|gb|DR906993.1|DR906993
EST:     GGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: GGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211292817|gb|FL187031.1|FL187031
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211294944|gb|FL187032.1|FL187032
EST:     CACAAAGAAGGGGCATGATGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|33094689|gb|CF054683.1|CF054683
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|32934317|gb|CF039129.1|CF039129
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|32935304|gb|CF040116.1|CF040116
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGCGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|33091320|gb|CF051314.1|CF051314
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211062769|gb|FL037852.1|FL037852
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211294946|gb|FL187034.1|FL187034
EST:     ACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: ACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211294949|gb|FL187037.1|FL187037
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
EST: gi|211281607|gb|FL229381.1|FL229381
EST:     TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAG                         AGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG
genomic: TACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacat ... ctgtttccagAGGAAGTTATTGCCGGTCTTGATCGTGCTGTGTTGAACATGAAGAAGGGCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAAAATTATCGGAAAGCTTCAGGATGGCGCGGTGTTTACAAAGAAGGGGCATGACGAAGAGCCATTTAAATTCAAGACCGATGAAGgtaagaacatccttttgtctttatatggggctcttggcctatcagtaaaaataataattcaggaaatcgacttgatcctgatatttagaataacatgtttcgtttgtattataatctgtttccag

- - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA