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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGCTTCTCACCTTGAGTCGATAGTGAGCATTCATAGGAGCCTCAGCTCTACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccattcttgcagaatatgaacttcaatcactgttaataactagtagtcggccaaagttttgactgatgtggtgaaatttctctttgttcag

Basic information

species Zea mays
transcript GRMZM2G052688_T01
intron # 4
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|32944789|gb|CF049608.1|CF049608
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
EST: gi|149027659|gb|EE286042.2|EE286042
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAAC
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAAC
EST: gi|76923847|gb|DV169691.1|DV169691
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
EST: gi|91872021|gb|EB401978.1|EB401978
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
EST: gi|78088729|gb|DV517122.1|DV517122
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
EST: gi|74233407|gb|DT641321.1|DT641321
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
EST: gi|78073936|gb|DV502370.1|DV502370
EST:     TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATG                         TTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG
genomic: TACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGG

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), 48 (downstream exon)
Score: 72

CCAGCTTCTCACCTTGAGTCGATAGTGAGCATTCATAGGAGCCTCAGCTCTACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGGTGGAGGAGAAATCTGACCAGATGAAATCTTACAACCCTGTTGCTTCAAA


Block sizes: 45 (upstream exon), 38 (downstream exon)
Score: 25

CCAGCTTCTCACCTTGAGTCGATAGTGAGCATTCATAGGAGCCTCAGCTCTACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGGTGGAGGAGAAATCTGACCAGATGAAATCTTACAACCCTGTTGCTTCAAA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 26

CCAGCTTCTCACCTTGAGTCGATAGTGAGCATTCATAGGAGCCTCAGCTCTACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGGTGGAGGAGAAATCTGACCAGATGAAATCTTACAACCCTGTTGCTTCAAA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 8

CCAGCTTCTCACCTTGAGTCGATAGTGAGCATTCATAGGAGCCTCAGCTCTACCGTCAGCACCATGATTGAACAACAGGATTCTCAAATTAACATTCATGgtacatccat ... ctttgttcagTTGCAAAGGCAGCATCTCATGGAACACCAGAATCAGGAAACAGAAGTGGGGTGGAGGAGAAATCTGACCAGATGAAATCTTACAACCCTGTTGCTTCAAA