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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactctccgctttcagtaatcccaacggtattcttcaaactttggaatttacatgcttcttttattcacgtttttttcgtgctcaacatccatttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG

Basic information

species Zea mays
transcript GRMZM2G138349_T03
intron # 1
splice site 3'
intron type U2

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|60672574|gb|DN475276.1|DN475276
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211169837|gb|FK962697.1|FK962697
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211166491|gb|FK962680.1|FK962680
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211169840|gb|FK962700.1|FK962700
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168166|gb|FK962693.1|FK962693
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168168|gb|FK962695.1|FK962695
EST:     GTAGGAAGGGGTAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168157|gb|FK962684.1|FK962684
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168159|gb|FK962686.1|FK962686
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|71768791|gb|DR966728.1|DR966728
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211169838|gb|FK962698.1|FK962698
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168160|gb|FK962687.1|FK962687
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168169|gb|FK962696.1|FK962696
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168161|gb|FK962688.1|FK962688
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168164|gb|FK962691.1|FK962691
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211166492|gb|FK962681.1|FK962681
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168167|gb|FK962694.1|FK962694
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168165|gb|FK962692.1|FK962692
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|31250107|gb|CD219131.1|CD219131
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168163|gb|FK962690.1|FK962690
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|50334443|gb|CO529569.1|CO529569
EST:     GTATGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168162|gb|FK962689.1|FK962689
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|78087464|gb|DV515857.1|DV515857
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168156|gb|FK962683.1|FK962683
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
EST: gi|211168158|gb|FK962685.1|FK962685
EST:     GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCG                         GATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT
genomic: GTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 40

GGAGCGGAGGAAGATCTCGGGCTCTCAGAGCTGCATCCTGAACCCATCGCGTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

GGAGCGGAGGAAGATCTCGGGCTCTCAGAGCTGCATCCTGAACCCATCGCGTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 78

GGAGCGGAGGAAGATCTCGGGCTCTCAGAGCTGCATCCTGAACCCATCGCGTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

GGAGCGGAGGAAGATCTCGGGCTCTCAGAGCTGCATCCTGAACCCATCGCGTAGGAAGGGGCAAAGGAGTCGGAGCTGATCCGGCAGTCGCTCTCTCTCGgtaagcaatt ... catttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttacatgcttcttttattcacgtttttttcgtgctcaacatccatttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG
                                           tccattt  CT-rich tract
           ttcttttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactctccgctttcagtaatcccaacggtattcttcaaactttggaatttacatgcttcttttattcacgtttttttcgtgctcaacatccatttggcagGATTGAGTACGATTTGACGCATTTGCGGCCGAGCTTTCTTGCACCCAAGATGAGTGGGCATGGTGACACTGCGACCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - ttacatg