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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttttctagaagtctctactggttcatatatttttatttgttttagtgttgggctgtgatgcactactattataaaaatatgttgatctgctacacattatccttttctttgtgcaacgctcagattcgtattatgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG

Basic information

species Zea mays
transcript GRMZM2G435244_T01
intron # 5
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|6827694|gb|AW331337.1|AW331337
EST:     TTTGGGCTATTGGANCTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAA                         GTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAATGCCAGCCCTGAGGTT
genomic: TTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAAgtaagttttt ... atgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTT




















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), 48 (downstream exon)
Score: 369

AGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAAgtaagttttt ... atgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 766

AGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAAgtaagttttt ... atgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 948

AGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAAgtaagttttt ... atgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 522

AGAAGATCAAGGACTGGAGCAACGTAGTTGTTGCCTATGAACCAGTTTGGGCTATTGGAACTGGTAAAGTTGCCACCCCAGCTCAGGCTCAGGAAgtaagttttt ... atgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacacattatccttttctttgtgcaacgctcagattcgtattatgttcccagGTGCACGCCTCCCTGAGGGATTGGCTAAAGACCAACGTCAGCCCTGAGGTTGCTGAATCTACTAGGATCATCTACGGAG
                                              tgttccc  CT-rich tract
                                         tattatgtt  TA-rich tract