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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgcgtgcttttttttttgagtaaactacatggcttcttcttgatgcatacttccaagtaagaaagaatcaaaactgtgtcagcttatggatttgcaaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG

Basic information

species Zea mays
transcript GRMZM5G824597_T02
intron # 5
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|37377388|gb|CF625291.1|CF625291
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|93012148|gb|EB637668.1|EB637668
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|76283432|gb|DV023000.1|DV023000
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|78180984|gb|DV551357.1|DV551357
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|94476028|gb|EB704986.1|EB704986
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|7844188|gb|AW787410.1|AW787410
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|7844190|gb|AW787412.1|AW787412
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|94476019|gb|EB704977.1|EB704977
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|12046853|gb|BF729005.1|BF729005
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|15177373|gb|BI398312.1|BI398312
EST:     ATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|7844189|gb|AW787411.1|AW787411
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|94479639|gb|EB708597.1|EB708597
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|60350072|gb|DN217045.1|DN217045
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
EST: gi|71326414|gb|DR799890.1|DR799890
EST:     ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAG                         TGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC
genomic: ACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCC

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: 49 (upstream exon), 49 (downstream exon)
Score: 34

GCTACAAAGCCAAAGCTTGTGACTGATAAGTTTCCAAGTGTGTCGGGTGCACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG


Block sizes: 42 (upstream exon), 45 (downstream exon)
Score: 31

GCTACAAAGCCAAAGCTTGTGACTGATAAGTTTCCAAGTGTGTCGGGTGCACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 20

GCTACAAAGCCAAAGCTTGTGACTGATAAGTTTCCAAGTGTGTCGGGTGCACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 16

GCTACAAAGCCAAAGCTTGTGACTGATAAGTTTCCAAGTGTGTCGGGTGCACCTCCAAGCTCTGATCAAATGATTGTTGCTGTACAGCAGCAAACACCAGgttgcgtgct ... aaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaagtaagaaagaatcaaaactgtgtcagcttatggatttgcaaacctgcagTGGCTTTACCTAGCAAAGTTCCTCCTGCTAAAGGTACGAAGCGCGTGGCCCCTTTGCCTCGGAG
               aatcaaaa  TA-rich tract