Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggagtgctttgatggttgtattatatcaccatattatgatatttttggagctgtggtttactaatatgacattttctgattatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG

Basic information

species Zea mays
transcript GRMZM2G060284_T01
intron # 3
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|116816147|gb|EC858853.1|EC858853
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATAGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|28187707|gb|CB179317.1|CB179317
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|211224212|gb|FK968311.1|FK968311
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|149085565|gb|EE175077.2|EE175077
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|13490745|gb|BG517509.1|BG517509
EST:     TATGCCGTGAAATAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|76937460|gb|DV175147.1|DV175147
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
EST: gi|211224214|gb|FK968313.1|FK968313
EST:     TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAG                         GTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT
genomic: TATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTT

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), 49 (downstream exon)
Score: 46

TAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 75

TAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

TAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 78

TAAATTTGACATGGAACCTCACAGCGATAATTTGGCGAACTATGGAAAGTTATGCCGTGAAAGAACACAAAAGTACATGGTTAAATCTAGACAAGTGCAGgtggagtgct ... ttatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatatttttggagctgtggtttactaatatgacattttctgattatttgtagGTACTTGACAATGACCATGGAATGAGCATGAGGCCAATGCCTGGCATTGTTGGTCTCATATCTTCTAGTTCAAAG
                                    attttctgattattt  TA-rich tract