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'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcatatctgcgtgtcataatcagcttaatcaggtcttttcttctgaatgtactgcttccatgcaagaagctcggcttatttatcttctatataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA

Basic information

species Zea mays
transcript GRMZM5G801369_T03
intron # 1
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|149075694|gb|EE164238.2|EE164238
EST:     ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAG                         ACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
genomic: ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
EST: gi|71301944|gb|DR787048.1|DR787048
EST:     ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAG                         ACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
genomic: ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
EST: gi|149062889|gb|EE157609.2|EE157609
EST:     ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAG                         ACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
genomic: ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
EST: gi|71438212|gb|DR819262.1|DR819262
EST:     ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAG                         ACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC
genomic: ACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTC

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: 48 (upstream exon), 41 (downstream exon)
Score: 61

CACGCGTACGCGCTCTCGTGGCGACGACTGGGTGATCGCCGCCGCCGCCGCCGCCACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA


Block sizes: 45 (upstream exon), 36 (downstream exon)
Score: 58

CACGCGTACGCGCTCTCGTGGCGACGACTGGGTGATCGCCGCCGCCGCCGCCGCCACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 134

CACGCGTACGCGCTCTCGTGGCGACGACTGGGTGATCGCCGCCGCCGCCGCCGCCACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 117

CACGCGTACGCGCTCTCGTGGCGACGACTGGGTGATCGCCGCCGCCGCCGCCGCCACCACGCACCACCAGGCCTTCACCGGCGACAAACACCACCAACAGgtaagcccac ... tataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtactgcttccatgcaagaagctcggcttatttatcttctatataacacagACACAAGTGCTTCAGTCATTATAGTGCCAGTACCATTCTGCCAGCGAGTTCCTTTGCCACAAAAAGATAACACTCGGATATCTCATGGCAAAACCTGGGA
                                            atataac  putative branch site (score: 117)
                                      tcttctat  CT-rich tract
                               ttatttatcttctata  TA-rich tract