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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtccatttgtctgcaaaagtgaacctggactccagctctaccgatcatgaagctttcgcgtgaaaacatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT

Basic information

species Zea mays
transcript GRMZM5G848603_T03
intron # 5
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|78110731|gb|DV529129.1|DV529129
EST:     CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGNAGAAG
genomic: CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|149005842|gb|EE040132.2|EE040132
EST:     CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|71430853|gb|DR811903.1|DR811903
EST:     CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|50331305|gb|CO526431.1|CO526431
EST:     GGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: GGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|78110730|gb|DV529128.1|DV529128
EST:     CCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: CCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|149107875|gb|EE292236.2|EE292236
EST:     CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
EST: gi|31353484|gb|CD437841.1|CD437841
EST:     CTACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAG                         ATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG
genomic: CGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAG

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: 44 (upstream exon), 48 (downstream exon)
Score: 14

CCGGAACTGGCTGTGGACAGCATTCACCTACACTGCCATGGTGGACTACCCGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 13

CCGGAACTGGCTGTGGACAGCATTCACCTACACTGCCATGGTGGACTACCCGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 18

CCGGAACTGGCTGTGGACAGCATTCACCTACACTGCCATGGTGGACTACCCGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 31

CCGGAACTGGCTGTGGACAGCATTCACCTACACTGCCATGGTGGACTACCCGACCCCAGCCAACTTCCTGGAGAACCTGCCTGCCTACCCAGTCAAGGAGgttgtccatt ... acatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacctggactccagctctaccgatcatgaagctttcgcgtgaaaacatctgcagATGTGCAAGACCATCGACGCGTTCCCCGCGGGCGCAGACGTCCTGGAGAAGGCGTTCGCGGCGGCGAGCCTGTACTACAACTACACGGGAGACCAGGCCT
                                          aaaacat  TA-rich tract