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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggaggcccttgtctgttgcatttctgatacaatgatgtctttgagttgaacgggttttcatgtgtttgtgttttccccccttaaaaaaattgcag

Basic information

species Zea mays
transcript GRMZM2G363460_T04
intron # 10
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|71312716|gb|DR792886.1|DR792886
EST:     ACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: ACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|60344992|gb|DN211965.1|DN211965
EST:     AGCCGATGTCCCCTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: AGCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|78075299|gb|DV503733.1|DV503733
EST:     ATAGGTCTTTTGGCAGTAAG                         CCATGGGAGATGCATTTGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: ATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|31354170|gb|CD438527.1|CD438527
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|110517843|gb|EE022430.1|EE022430
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|20301072|gb|BQ164015.1|BQ164015
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCA-GCAGTATTCACAACAGAGGCCTGGTTATGGATCCAA
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTC-GTATTCACAACAGAGGCCTGGTTATGGATCCAA
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|76281031|gb|DV020599.1|DV020599
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|76912797|gb|DV164885.1|DV164885
EST:     AGCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: AGCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
EST: gi|78109255|gb|DV527671.1|DV527671
EST:     CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG                         CCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC
genomic: CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAAC

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: 47

CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAACTCCCAGTTGAGTGATGATGGATCATACTCTGATGCCCAGGACAGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAACTCCCAGTTGAGTGATGATGGATCATACTCTGATGCCCAGGACAGCTATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 54

CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAACTCCCAGTTGAGTGATGATGGATCATACTCTGATGCCCAGGACAGCTATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAGgtgagaggag ... aaaattgcagCCATGGGAGATGCATTCGTATTCACAACAGAGGCCTGGTTATGGATCCAACTCCCAGTTGAGTGATGATGGATCATACTCTGATGCCCAGGACAGCTATG