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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgagttatggagtgatatgcggtttgaaatttcgtattgttattgcccaattttggttacacaagtttgtgttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG

Basic information

species Zea mays
transcript GRMZM2G111713_T02
intron # 3
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|211203210|gb|FL341871.1|FL341871
EST:     GCATGATMGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
genomic: GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
EST: gi|211264640|gb|FL311733.1|FL311733
EST:     GCATGATTGGCCACAATCTCGAGGGGCCGTTGCMAGTNCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATSATGCTAGACCGATGTCAACAGCA
genomic: GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
EST: gi|211157788|gb|FL363018.1|FL363018
EST:     CATGATTGGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
genomic: CATGATT-GGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
EST: gi|211337834|gb|FL344315.1|FL344315
EST:     GCATGATTGGCCACAATCTCGAGGGGCCGTTNC-AGTCCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
genomic: GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
EST: gi|211474786|gb|FL319644.1|FL319644
EST:     GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
genomic: GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
EST: gi|211481012|gb|FL352018.1|FL352018
EST:     GCATGATKGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAG                         GTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA
genomic: GCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCA

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: 76

GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 48

GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 41

GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 61

GTTTTGCAAGCTTGACGTACAATGCCAGCAGCATGATTGGCCACAATCTCGAGGGGCCGTTGCCAGTCCACATTGTGAAGgttcgagtta ... gttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatttcgtattgttattgcccaattttggttacacaagtttgtgttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG
                                            tgttcct  CT-rich tract
         tattgttatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgagttatggagtgatatgcggtttgaaatttcgtattgttattgcccaattttggttacacaagtttgtgttcctgcagGTTCTGGATCTCGTAGTACATATGAATCATGCTAGACCGATGTCAACAGCAGCAGCATCAAAGGTGCCTGTTGGAGCCCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG