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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaatgatcactctacctatgctcaaaattcaatgtataatagtgtgaatatattttttatgacttttctctccaaactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG

Basic information

species Zea mays
transcript GRMZM2G047867_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 6
gtaagaatgatcactctacctatgctcaaaattcaatgtataatagtgtgaatatattttttatgacttttctctccaaactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG
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gtaagaagcatcacttta----tgctttagagtagaattgtcaaattattgttattttaatgattattatgctctc-aacctatgcagGTCTGTAAAGATTTCTTCCCACAACTATCTGTTGGATTCAAAGATCCCCGTGTTCAACTTCATGTTGGTGACG
















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|71757237|gb|DR955174.1|DR955174
EST:     ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGAT                         GTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
EST: gi|5895598|gb|AW036844.1|AW036844
EST:     ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGAT                         GTTTGCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
EST: gi|88757916|gb|DY542057.1|DY542057
EST:     ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGAT                         GTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
EST: gi|5791184|gb|AI977976.1|AI977976
EST:     GAGATTGATCAACTAGATATTGAT                         GTTTGCAAAGAAGTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: GAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
EST: gi|88757557|gb|DY541698.1|DY541698
EST:     ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGAT                         GTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: ATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
EST: gi|5847488|gb|AW000567.1|AW000567
EST:     AAACTATTGATATATGTGAGATTGATCAACTAGTTATTGAT                         GTTTGCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT
genomic: AAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGT

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), 45 (downstream exon)
Score: 29

GGTTGTTGGAGGTGGTGATGGTGGTGTACTGCGCGAAATAGCCAGACATGATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 10

GGTTGTTGGAGGTGGTGATGGTGGTGTACTGCGCGAAATAGCCAGACATGATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 83

GGTTGTTGGAGGTGGTGATGGTGGTGTACTGCGCGAAATAGCCAGACATGATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

GGTTGTTGGAGGTGGTGATGGTGGTGTACTGCGCGAAATAGCCAGACATGATTCAGTGGAAACTATTGATATATGTGAGATTGATCAACTAGTTATTGATgtaagaatga ... aactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgtataatagtgtgaatatattttttatgacttttctctccaaactatgcagGTTTCCAAAGAATTCTTTCCAAACTTATCCATTGGATTCAAAGATCCTCGTGTCCGACTTCATGTTGGTGATG
     tataatagtgtgaata  TA-rich tract