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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaacctttgctcggatgagttctttcgttcaaagtgaggattcggtagtggtgttctcaatcaaacccaaatcgatgttttcgccattccgatccagttaaccgtccatttttgtgctgcgtggtattacccagctaacgcaatccaatctatccggccttggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA

Basic information

species Zea mays
transcript GRMZM2G124051_T01
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|71429759|gb|DR810809.1|DR810809
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|149039469|gb|EE046609.2|EE046609
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532376|gb|FL244241.1|FL244241
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211529376|gb|FL244234.1|FL244234
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532377|gb|FL244242.1|FL244242
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|148947123|gb|EC892433.2|EC892433
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532380|gb|FL244245.1|FL244245
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532373|gb|FL244238.1|FL244238
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532371|gb|FL244236.1|FL244236
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|149078953|gb|EE167793.2|EE167793
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|149082745|gb|EE171964.2|EE171964
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
EST: gi|211532375|gb|FL244240.1|FL244240
EST:     CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTG                         GGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG
genomic: CGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAG

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: 42 (upstream exon), 47 (downstream exon)
Score: 28

CGCGAGCACAGCTCCGCCGCCACCGCCCCCTTCTCATCCGCGGTCTCCTCCGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA


Block sizes: 23 (upstream exon), 43 (downstream exon)
Score: 7

CGCGAGCACAGCTCCGCCGCCACCGCCCCCTTCTCATCCGCGGTCTCCTCCGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 17

CGCGAGCACAGCTCCGCCGCCACCGCCCCCTTCTCATCCGCGGTCTCCTCCGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 35

CGCGAGCACAGCTCCGCCGCCACCGCCCCCTTCTCATCCGCGGTCTCCTCCGCCTGCTGCATCTCTATCGATCTAGCGGGACTGGCTCCTTCCCGTGCTGgttagtaacc ... ggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcgtggtattacccagctaacgcaatccaatctatccggccttggtttgatagGGTCCTTCGTCAATCGTCAGCGCGCAAGATCGGCACTTGTGTACATCTGAGCAGTTTCCGGTGCCCTAATTCAGGCGCGGGCGTTGTTGGGTTTTCGATA
                agctaac  putative branch site (score: 35)
                              aatctat  TA-rich tract