Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttgccttctggcttcgcctttttgctgttgtaaacccgaaattcgagttggctgttagagtttttgcaattgtctttatagcattgatacattgcattttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG

Basic information

species Zea mays
transcript GRMZM2G052479_T01
intron # 7
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|148961906|gb|EE012693.2|EE012693
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|94472720|gb|EB701678.1|EB701678
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|211089074|gb|FL456421.1|FL456421
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|149098517|gb|EE184497.2|EE184497
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|76930618|gb|DV172456.1|DV172456
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|148938520|gb|EC882841.2|EC882841
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|101386886|gb|EB815460.1|EB815460
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|71760018|gb|DR957955.1|DR957955
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
EST: gi|76930616|gb|DV172454.1|DV172454
EST:     CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATG                         GTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA
genomic: CAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTA

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: 45 (upstream exon), 49 (downstream exon)
Score: 42

GCTGGCCTCAAGATAATACAGTTGTACAGGGAAGGATACAGGCAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 92

GCTGGCCTCAAGATAATACAGTTGTACAGGGAAGGATACAGGCAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 46

GCTGGCCTCAAGATAATACAGTTGTACAGGGAAGGATACAGGCAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 63

GCTGGCCTCAAGATAATACAGTTGTACAGGGAAGGATACAGGCAGGACTGGGAATTGTCATTCGAGAAGAACACCAGGACAAAAGGCGGATGgtatgtttgc ... ttttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttagagtttttgcaattgtctttatagcattgatacattgcattttctctagGTATCAAGGGGGGTTAATTGTTGCAGGTCCAGGTATCGATAACATCCTGTACATCCACAAG
                              cattgat  putative branch site (score: 63)
                                           cattttctct  putative PPT
                     tctttata  TA-rich tract