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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTTTCTTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtagctgcatgatttgtgttctcctgccccattgatgtttcggagccttacatgttctgttttcttggggaaaaatgtgttcctttgcaaggtaacctttctaagtttttttgtgctttgataattgatactcaatgcag

Basic information

species Zea mays
transcript GRMZM2G130548_T01
intron # 4
splice site 5'
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|5455802|gb|AI833492.1|AI833492
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|12971278|gb|BG267403.1|BG267403
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|30052458|gb|AI065747.2|AI065747
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|213179400|gb|FM185674.1|FM185674
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|29945353|gb|CB815596.1|CB815596
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|78027480|gb|DV495867.1|DV495867
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|111145857|gb|EE258097.1|EE258097
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|22489673|gb|BU049596.1|BU049596
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|211320303|gb|FL454022.1|FL454022
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|18649960|gb|BM498779.1|BM498779
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTACCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|32865321|gb|CF005003.1|CF005003
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
EST: gi|211023896|gb|FL457615.1|FL457615
EST:     TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAG                         GAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT
genomic: TTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGT

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: 49 (upstream exon), 48 (downstream exon)
Score: 181

GGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTTTCTTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

GGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTTTCTTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 116

GGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTTTCTTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG


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

GGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTTTCTTCAATCCAGAATATCAGTACTAGGCAACCATTTTCCCTTCACTTGCCAGgtgagcgtag ... ctcaatgcagGAATGTGCTAGGATCGGTTTGGAGGAAGATGTCTGGATATTAGGATTGCGTTTTGCACCTACTGAATCGATGATATTGTGTAGATGGACAACCATAATTG