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

gtaagatccaccctattcataaacagataagtgctcacttaatgatttgtattaacacattttatacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG

Basic information

species Zea mays
transcript GRMZM2G028307_T02
intron # 10
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|32941912|gb|CF046731.1|CF046731
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACATTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
EST: gi|32932602|gb|CF037414.1|CF037414
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACATTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
EST: gi|32940378|gb|CF045197.1|CF045197
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACATTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
EST: gi|32945347|gb|CF050166.1|CF050166
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACATTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
EST: gi|74237283|gb|DT645197.1|DT645197
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
EST: gi|89760464|gb|DY688865.1|DY688865
EST:     GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATC                         GGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC
genomic: GATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTC

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: 49 (upstream exon), 49 (downstream exon)
Score: 105

CACAAGATGGGAAACCAGATCATATATGCAGGAACTATGAAATACTGAATGATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 49

CACAAGATGGGAAACCAGATCATATATGCAGGAACTATGAAATACTGAATGATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 32

CACAAGATGGGAAACCAGATCATATATGCAGGAACTATGAAATACTGAATGATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CACAAGATGGGAAACCAGATCATATATGCAGGAACTATGAAATACTGAATGATAAAAATGTCTCATTTTGCCTCGGAAAAACAAAACGTTTTCTTGCATCgtaagatcca ... tacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacagataagtgctcacttaatgatttgtattaacacattttatacattgtagGGATGTCCTTACCATGGACACCAAGGAACACCAATCAAAGTTTCATATTTCAGTTACAAACACTGATGATACTTGTTTGGATGCATCTGCTGGTCGAAGG
                              tattaac  putative branch site (score: 106)
                   ttaatgatttgtatta  TA-rich tract