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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtacgtgcgtgtcatgcatgtccgatcctacgtaccaacgctctctctctctacctctctcccgatgacactgcatgcatgtcaatataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT

Basic information

species Zea mays
transcript GRMZM2G118063_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 9
gtacgta-cgtgcgtgtcatgcatgtccgatcctacgtaccaacgctctctctctctacctctctcccgatgacactgcatgcatgtcaatataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT
|| |  |   |||    ||| | |     ||    |  |     |||  |    | |    |     | |   || | |   |  ||    ||    |||||||||||| || |||||||| ||||| ||||||||||||||||| ||||| |||||||| |||||||||||||  ||||| |||||||||||||||
gtgcccaatttgccccccatccctagggaatttatccaatt--tgctgaccaaattttatacgtgatcaaattcattcctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT

upper sequence: GRMZM2G118063_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ19972 (Selaginella moellendorffii), 3'ss of exon 9
gtacgtacgtgcgtgtcatgcatgtccgatcctacgtaccaacgctctctctctctacctctctcccgatgacactgcatgcatgtcaata--taattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT
                                   ||| ||  ||| ||  |   | | ||     ||| |    || ||   | |   |   |  |||||||||||||| ||||||||||||||    || ||||| |||||||| || || || || | ||| |  |||||| | ||||| ||||| |||||||| 
-----------------------------------gtaacagagct-tcgtttgatccatcaaaatcga-gtttttgtatcggttttcttggctttttgcagTGGGACATTCTCTCCAACGGTGGAATGGTGCAAGAGATGGCTCACATCGCCAAAGGACAGGATCCAGGCAACAGTGTCTCTCTTCTCCGTGTCAAC
















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|26558595|gb|CA830830.1|CA830830
EST:     CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
genomic: CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
EST: gi|87156118|gb|DY400907.1|DY400907
EST:     CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGATATGGCTCATATTGCT
genomic: CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
EST: gi|22472184|gb|BU036664.1|BU036664
EST:     CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
genomic: CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
EST: gi|76017721|gb|DT944891.1|DT944891
EST:     CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
genomic: CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
EST: gi|5566756|gb|AI881622.1|AI881622
EST:     CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA
genomic: CGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCA

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), 48 (downstream exon)
Score: 144

GCCGCCGGGCATCGTCCTCAACGCTGCCACCTCCTTCTGGCTGCCTGTCCCGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT


Block sizes: 38 (upstream exon), 39 (downstream exon)
Score: 10

GCCGCCGGGCATCGTCCTCAACGCTGCCACCTCCTTCTGGCTGCCTGTCCCGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 1

GCCGCCGGGCATCGTCCTCAACGCTGCCACCTCCTTCTGGCTGCCTGTCCCGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 40

GCCGCCGGGCATCGTCCTCAACGCTGCCACCTCCTTCTGGCTGCCTGTCCCGCCCAAGAGGGTCTTCGACTTCCTCCGCGACGAGACCTCTCGCAGCGAGgtacgtacgt ... ataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctctctctacctctctcccgatgacactgcatgcatgtcaatataattgcagTGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT
                                     atgtcaatataatt  TA-rich tract