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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttcctcatctcacatccctcatttgtcctccatacaatcccgaattccactgcttacctcttcatctccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG

Basic information

species Zea mays
transcript GRMZM2G118316_T01
intron # 1
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|76922542|gb|DV169052.1|DV169052
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|149101262|gb|EE187374.2|EE187374
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|78088193|gb|DV516586.1|DV516586
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|93017256|gb|EB642776.1|EB642776
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|211523404|gb|FL361945.1|FL361945
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTTTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|71757145|gb|DR955082.1|DR955082
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|211149678|gb|FL347659.1|FL347659
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|71771526|gb|DR969463.1|DR969463
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|211401713|gb|FL219582.1|FL219582
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|71427931|gb|DR808981.1|DR808981
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|91049687|gb|EB160105.1|EB160105
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTTTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|211401714|gb|FL219583.1|FL219583
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|91049823|gb|EB160241.1|EB160241
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
EST: gi|71769072|gb|DR967009.1|DR967009
EST:     CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACG                         CGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC
genomic: CGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACC

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: 43

CTGTGCAAAGTAGGGTTTCCACCGGGACACAGGCCGCCTCCATCCCATGGCGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 19

CTGTGCAAAGTAGGGTTTCCACCGGGACACAGGCCGCCTCCATCCCATGGCGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 16

CTGTGCAAAGTAGGGTTTCCACCGGGACACAGGCCGCCTCCATCCCATGGCGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 20

CTGTGCAAAGTAGGGTTTCCACCGGGACACAGGCCGCCTCCATCCCATGGCGCGCGCCGCCGCCTCCAGGCTCGCCGCCGTGGCGAACTCTTCCTCTACGgtgagcttcc ... ccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtcctccatacaatcccgaattccactgcttacctcttcatctccgttgccagCGCGAGTTGTTCGCCCGCCACCTCGCCGCCGCTGCCGCCTCGGCGTGGACCGCACCGCCGCGTCTGCCTGAACCAG
                            tgcttac  putative branch site (score: 20)
                              cttacctcttcatctc  CT-rich tract
         atacaat  TA-rich tract