Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcataataatgaatatgataattttatattgcatttcctttatccagcttactatcacaggtgaagaattacattttatttgtttatagttgctgatttcatatgtctatttcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT

Basic information

species Zea mays
transcript GRMZM2G136293_T01
intron # 6
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|32934389|gb|CF039201.1|CF039201
EST:     TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAG                         CATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
genomic: TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
EST: gi|37385535|gb|CF629914.1|CF629914
EST:     TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAG                         CATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
genomic: TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
EST: gi|5791256|gb|AI978048.1|AI978048
EST:     TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAG                         CATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
genomic: TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
EST: gi|113702216|gb|EE679720.1|EE679720
EST:     TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAG                         CATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG
genomic: TTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTG

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: 44 (upstream exon), 46 (downstream exon)
Score: 15

CTTGACAGGGCCTCAGAGCTCAATATTAGCTGGGATCCTGCTGAACAAAGTTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 26

CTTGACAGGGCCTCAGAGCTCAATATTAGCTGGGATCCTGCTGAACAAAGTTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 59

CTTGACAGGGCCTCAGAGCTCAATATTAGCTGGGATCCTGCTGAACAAAGTTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 53

CTTGACAGGGCCTCAGAGCTCAATATTAGCTGGGATCCTGCTGAACAAAGTTCACAGTCAACAAAACATAGTCAGGAGGATGAACACAGGAACCAACCAGgtatgcataa ... tcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattacattttatttgtttatagttgctgatttcatatgtctatttcttgtgcagCATCGATTAGTCTGGGGAAACGAACTCATGAGTTGCATGGCTCGAGTTCTGGTAATAGGGGGGATAATAGGGGGCACCGATCTAACAAGCGAGACCGGGT
                        tgctgat  putative branch site (score: 53)
                                       tctatttctt  putative PPT
      attttatttgtttata  TA-rich tract