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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccaccactaccattctcccgtggacggcctagctcctgggaaactgcattctcgctgcttaactgctagcattgctcatcgtgtgcgcaattgtaatcgtgacgatgcattccgactgcag

Basic information

species Zea mays
transcript GRMZM5G837018_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G837018_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g56260.1 (Oryza sativa), 5'ss of exon 1
GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccaccactaccattctcccgtgga-cggcctagctcctgggaaactgcattctcgctgcttaactgctagcat--tgctcatcgtgtgcgcaattgtaatcgtgacgatgcattccgactgcag
                                  ||||||||||    | ||||||||||||||||||||||||| ||||||||||||||||||||||||||     |     | | |||| |  || | |||      |   |  |     |    |   || ||   || | | ||  ||||  | |         ||  |   || |  |||  |  |  ||||||
----------------------------------GAAGGTTCCT----GGCAATGCCGAGCATCCGAGCTCCGGCTTCCAAGCAGACGGCCACGCTACAGgtagattatag--atccttctgcgatgaaacggatggaatggagtaatttctcgcgattcttgattttttgttgggatgatgctgcttgctctgttgcttcgatgtgtaatcatgtgtctct-ctgcag
















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|4630567|gb|AI621441.1|AI621441
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
EST: gi|149069078|gb|EE157805.2|EE157805
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
EST: gi|19058353|gb|BM737020.1|BM737020
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
EST: gi|76926761|gb|DV170984.1|DV170984
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
EST: gi|78090427|gb|DV518801.1|DV518801
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
EST: gi|83278868|gb|DV942876.1|DV942876
EST:     CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAG                         GTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG
genomic: CAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGG

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), 49 (downstream exon)
Score: 57

GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGGCATATTATACAGGTCATTGATGACAAG


Block sizes: 45 (upstream exon), 32 (downstream exon)
Score: 19

GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGGCATATTATACAGGTCATTGATGACAAG


Block sizes: 33 (upstream exon), 43 (downstream exon)
Score: 5

GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGGCATATTATACAGGTCATTGATGACAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 16

GCATCTTTTTTGGAGGGCTCGTCTCGGCTGGCACGAAGGTTCCTCGCGGACAATGCCGAGCATCCGAGCTCCGGCGTCCAAGCAGACGGCCACGCTACAGgtgcgccacc ... ccgactgcagGTGGCTGTCAAGTGCAGGCCATTGACCGACACCGAGCAGCGGCGTTCGCGGCATATTATACAGGTCATTGATGACAAG