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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgcgggatcgctcccagaaacgtccgagttgcagttcccaatttttttctctttctttccaaaatcattttctgaagaattctccccaaatcctgttcacttctttggttcggggttgacggggttctttgttgctaacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG

Basic information

species Zea mays
transcript GRMZM5G823750_T02
intron # 1
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|211540347|gb|FL091515.1|FL091515
EST:     GCA-CGTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: GCAGC-TGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211540346|gb|FL091514.1|FL091514
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|78116158|gb|DV534546.1|DV534546
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|78120227|gb|DV538611.1|DV538611
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211540349|gb|FL091517.1|FL091517
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|76013572|gb|DT940742.1|DT940742
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211131059|gb|FL391857.1|FL391857
EST:     GCA--TGCGGGTACATGATGAGCCATTATTTTGGTACMCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: GCAGCTGCGG-TACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|29576943|gb|CB617055.1|CB617055
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GTGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543360|gb|FL091529.1|FL091529
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543361|gb|FL091530.1|FL091530
EST:     CGCAGCTGCGGTACATGATGAGCCGKTATTTTGGTACCCCACCTAGCAAG                         GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|101385030|gb|EB814560.1|EB814560
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|84980380|gb|DW530729.1|DW530729
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543355|gb|FL091524.1|FL091524
EST:     CGCAGCTGCGGTACATGATAAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543350|gb|FL091519.1|FL091519
EST:     GCA-CTGCGGTTACATGATAAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: GCAGCTGCGG-TACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543352|gb|FL091521.1|FL091521
EST:     CGCAGCTGCGGTACATGATAAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211540348|gb|FL091516.1|FL091516
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGCGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543357|gb|FL091526.1|FL091526
EST:     CGCA-STGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTT-GAGGACAAAG
EST: gi|211543362|gb|FL091531.1|FL091531
EST:     CGCAGCTGCGGTACATGATAAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543353|gb|FL091522.1|FL091522
EST:     GCAGCTGCGGTACATGATSGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: GCAGCTGCGGTACATGAT-GAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543349|gb|FL091518.1|FL091518
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|24462553|gb|BM660084.1|BM660084
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|76011928|gb|DT939098.1|DT939098
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|91050221|gb|EB160639.1|EB160639
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|93011924|gb|EB637444.1|EB637444
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|78116574|gb|DV534961.1|DV534961
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543359|gb|FL091528.1|FL091528
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543351|gb|FL091520.1|FL091520
EST:     GCA-CGTGCGGTACATGATAAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: GCAGC-TGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|211543354|gb|FL091523.1|FL091523
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
EST: gi|33770746|gb|CF273040.1|CF273040
EST:     CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAG                         GAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
genomic: CGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 86

AACACGCATCGACCCTACGACTACGAGTAGCGAGAGAGGATTGATGGCGGCGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG


Block sizes: 46 (upstream exon), 37 (downstream exon)
Score: 32

AACACGCATCGACCCTACGACTACGAGTAGCGAGAGAGGATTGATGGCGGCGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 61

AACACGCATCGACCCTACGACTACGAGTAGCGAGAGAGGATTGATGGCGGCGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 68

AACACGCATCGACCCTACGACTACGAGTAGCGAGAGAGGATTGATGGCGGCGCAGCTGCGGTACATGATGAGCCATTATTTTGGTACCCCACCTAGCAAGgttcgcggga ... aacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgttcacttctttggttcggggttgacggggttctttgttgctaacgaggcagGAGGTGATCCAAGATCTGTACTACGCCTTGAGGACAAAG
                                         tgctaac  putative branch site (score: 68)