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

gtataaactgtcctaattttattactacaaactgccctagttccttttcacacagcttaccgaatccagattgtgttagcgacaaatcaaacattatattcttacatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT

Basic information

species Zea mays
transcript GRMZM2G044382_T01
intron # 8
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|149071131|gb|EE159530.2|EE159530
EST:     CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAG                         ATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
genomic: CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
EST: gi|16927376|gb|BM080445.1|BM080445
EST:     CGCCATTCACGAG                         ATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
genomic: CGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
EST: gi|71315035|gb|DR794138.1|DR794138
EST:     CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAG                         ATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
genomic: CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
EST: gi|60347969|gb|DN214942.1|DN214942
EST:     CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAG                         ATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
genomic: CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
EST: gi|148971591|gb|EE022307.2|EE022307
EST:     CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAG                         ATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA
genomic: CAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAA

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: 46 (upstream exon), 49 (downstream exon)
Score: 127

TTGTCAAGGCCAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 21

TTGTCAAGGCCAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 26

TTGTCAAGGCCAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 40

TTGTCAAGGCCAGGGAAGCTGCGTCCCTGGGATGGCCCTTTCCTTTGTCACAGCTGCCAGGAAAAGAAAGAGGCGATGGAGGGGAAGCGCCATTCACGAGgtataaactg ... acatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accgaatccagattgtgttagcgacaaatcaaacattatattcttacatctgcagATTCCTCGTCCAGAAATAGCGGGTCAAGTGAATCGTGACTGAAGCCGAGAATCATCTTGAGGCAAACGCCTAGCGGTGTGACGAGCTAATTATCGTTGCT
                                        ttcttac  putative branch site (score: 40)
                                        ttcttac  CT-rich tract
                         aaatcaaacattatat  TA-rich tract