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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtagtacctcgtgatgctttgctcgccggattaattgaattgaatctgaatttgaactgtatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAAAGGTGCATCTGAAACAGGTAGACCTGATTGGGCTGGGATCTGGGCCGGA

Basic information

species Zea mays
transcript GRMZM2G043893_T02
intron # 2
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|89247434|gb|DY619220.1|DY619220
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|148991872|gb|EE033466.2|EE033466
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|76913696|gb|DV165228.1|DV165228
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|149001042|gb|EE038291.2|EE038291
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAGA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|74236862|gb|DT644776.1|DT644776
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|148958193|gb|EC904398.2|EC904398
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71436982|gb|DR818032.1|DR818032
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71774295|gb|DR972173.1|DR972173
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
EST: gi|71318210|gb|DR795867.1|DR795867
EST:     TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTG                         GAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA
genomic: TGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAA

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 40 (downstream exon)
Score: 28

GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAAAGGTGCATCTGAAACAGGTAGACCTGATTGGGCTGGGATCTGGGCCGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86

GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAAAGGTGCATCTGAAACAGGTAGACCTGATTGGGCTGGGATCTGGGCCGGA


Block sizes: 15 (upstream exon), 35 (downstream exon)
Score: 1

GCCAGGGCTGCTCGGGCCACCAGCGCCGCCATCCTTGTCGCCGACCCCGCTGTGGTCCGACCGGAGTCCAGGCTGAATGCTGCCGCGGCAATTGCTTCTGgtactgtagt ... tatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAAAGGTGCATCTGAAACAGGTAGACCTGATTGGGCTGGGATCTGGGCCGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctttgctcgccggattaattgaattgaatctgaatttgaactgtatattgcagGAACTGTGCTTGGACTGTACGAGGACAACAGATACAAGTCCGAGTGGGAAAAGGTGCATCTGAAACAGGTAGACCTGATTGGGCTGGGATCTGGGCCGGA
              gattaat  putative branch site (score: 1)
               attaattgaattgaat  TA-rich tract