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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacattatttgtctagttgggtgatttgggccacttgactttttgtttgtttgtcttgaagttgtctattgtgtctcataacatttgtggacttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG

Basic information

species Zea mays
transcript GRMZM2G002859_T01
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|71307047|gb|DR789678.1|DR789678
EST:     CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|149070323|gb|EE158722.2|EE158722
EST:     CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|33091909|gb|CF051903.1|CF051903
EST:     AAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAATTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: AAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|148986436|gb|EE030178.2|EE030178
EST:     CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|40335185|gb|CK369255.1|CK369255
EST:     CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|60356623|gb|DN223596.1|DN223596
EST:     CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTG                         GTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: CCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
EST: gi|37380473|gb|CF627052.1|CF627052
EST:     TTGACCTTGCAGCGTCTTATTGCATTG                         G-TGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA
genomic: TTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAA

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), 46 (downstream exon)
Score: 98

GAAATCGAATATGGGGGTATTGGGCAAAGAAGCTGTTGCAGCAATGACTGCCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 58

GAAATCGAATATGGGGGTATTGGGCAAAGAAGCTGTTGCAGCAATGACTGCCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 49

GAAATCGAATATGGGGGTATTGGGCAAAGAAGCTGTTGCAGCAATGACTGCCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG


Block sizes: 48 (upstream exon), 38 (downstream exon)
Score: 52

GAAATCGAATATGGGGGTATTGGGCAAAGAAGCTGTTGCAGCAATGACTGCCGTTGAGGCCCAACAGCAAAGATTGACCTTGCAGCGTCTTATTGCATTGgtacattatt ... ttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgtcttgaagttgtctattgtgtctcataacatttgtggacttaattgaagGTTGAATCAGAGAGAAACTACCACCAAAAGGTCCTACAAATTCTTGATCAACTTGAGAGAGAG
                              ataacattt  TA-rich tract