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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggacatgaaacctcgattttttatgtgtcaaatttaatttcatcattcgtgttaatttcacttactagtgtctgctttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT

Basic information

species Zea mays
transcript GRMZM2G043862_T01
intron # 11
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|60394527|gb|DN227397.1|DN227397
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|26457476|gb|CA829059.1|CA829059
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|211216600|gb|FL362617.1|FL362617
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|9953937|gb|BE640520.1|BE640520
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|86473094|gb|DY239464.1|DY239464
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|78180885|gb|DV551258.1|DV551258
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAAAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|7844623|gb|AW787845.1|AW787845
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|211049730|gb|FL339082.1|FL339082
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|149100035|gb|EE186087.2|EE186087
EST:     CTTCATTTGGCACTGATTTTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|113701275|gb|EE678779.1|EE678779
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|78544483|gb|DV621981.1|DV621981
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|6918321|gb|AW399851.1|AW399851
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|40303469|gb|CK347856.1|CK347856
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|110532724|gb|EE036904.1|EE036904
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|8318652|gb|BE025397.1|BE025397
EST:     CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG
EST: gi|110515665|gb|EE020253.1|EE020253
EST:     CTTCATTTGGCACTGATTTTGCCTGGTTTGGTGCAAAGATGATCAGCAAC                         GTGAGTACTTTCACTGAGGCATGGTGGGCAAAGAAGAAACAATTCCGTCAG
genomic: CTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAG

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: 46 (upstream exon), 42 (downstream exon)
Score: 12

TCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT


Block sizes: 47 (upstream exon), 41 (downstream exon)
Score: 24

TCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 13

TCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT


Block sizes: 46 (upstream exon), 40 (downstream exon)
Score: 22

TCACCAACTTCTTCCACCTTATATGTCAGAAGGAATAAGAGTACTCCCCCCTTCATTTGGCACTGATTCTGCCTGGTTTGGTGCAAAGATGATCAGCAACgtaaggacat ... ttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaatttcatcattcgtgttaatttcacttactagtgtctgctttaactttagGTGAGTACTTTCACTGAGGCATGGTGTGCAAAGAAGAAACAATTCCGTCAGAAGACAGGCCGGAGTGGTACATTGTTTGCCAATTCCTGGTAATGAAAAT
                                       tctgcttt  CT-rich tract
                                            tttaacttta  TA-rich tract