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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtctcggtctcgatttgccttttggccgcctctgattgatcgtgtttctccagcatctggacctgaccatgcgttgttttgttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG

Basic information

species Zea mays
transcript GRMZM2G024686_T01
intron # 2
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|149013851|gb|EE043331.2|EE043331
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|71433314|gb|DR814364.1|DR814364
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|93016258|gb|EB641778.1|EB641778
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|94477550|gb|EB706508.1|EB706508
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|148945409|gb|EC890633.2|EC890633
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|71757140|gb|DR955077.1|DR955077
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|91877619|gb|EB407576.1|EB407576
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|149108954|gb|EE293062.2|EE293062
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|148963115|gb|EE014078.2|EE014078
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
EST: gi|149000754|gb|EE037974.2|EE037974
EST:     AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAG                         GACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
genomic: AAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG

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: 47 (upstream exon), 41 (downstream exon)
Score: 111

GCCGGCGAGAAGGCGGTGAGCTGCGGCGCCCCCAAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 50

GCCGGCGAGAAGGCGGTGAGCTGCGGCGCCCCCAAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG


Block sizes: 48 (upstream exon), 41 (downstream exon)
Score: 43

GCCGGCGAGAAGGCGGTGAGCTGCGGCGCCCCCAAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG


Block sizes: 43 (upstream exon), 41 (downstream exon)
Score: 21

GCCGGCGAGAAGGCGGTGAGCTGCGGCGCCCCCAAGGCGTCCGAAATCCCTGAGCTCGCTGTCATCAAGGACCTGCATCTTAGgtgtgtctcg ... ttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatcgtgtttctccagcatctggacctgaccatgcgttgttttgttgttgccagGACGGTTGATGAGCTCGGTTTAGATAGGTCGATTGTTTCAG
                        acctgac  putative branch site (score: 21)
                                        ttttgtt  putative PPT
                                     ttgtttt  TA-rich tract