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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgttgctcccaactcctctgcgtatatgtagcttgcaagtacagtctgaagcgcgctgactgcagggggggtgtcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT

Basic information

species Zea mays
transcript GRMZM2G110834_T01
intron # 12
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|42491818|gb|CK700864.1|CK700864
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|60397677|gb|DN230493.1|DN230493
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|166577869|gb|EG126841.1|EG126841
EST:     ATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGC
genomic: ATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGC
EST: gi|91869156|gb|EB400279.1|EB400279
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|84969395|gb|DW467833.1|DW467833
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|211076057|gb|FL474784.1|FL474784
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|6672167|gb|AW282342.1|AW282342
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|74231927|gb|DT639841.1|DT639841
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|71318559|gb|DR796040.1|DR796040
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATTTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|113841671|gb|DW967677.1|DW967677
EST:     CTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTACGTGGCTGATCACATTCTGGTCAGCA
genomic: CTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTT-CGTGGCTGATCACATTCTGGTCAGCA
EST: gi|76910092|gb|DV163696.1|DV163696
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
EST: gi|211529174|gb|FL238578.1|FL238578
EST:     CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCACCAAGTTTGGACACG                         GTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG
genomic: CCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAG

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: 43 (upstream exon), 48 (downstream exon)
Score: 65

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 43

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 75

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 34

CAAACCATTTAAAAAGGTGGGATCCTTCTGCTGGCTTTCCCTGGCTATATGCATTGTGGAGCTCCTAATCTGCATCAAGTTTGGACACGgtgagtgttg ... tcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcttgcaagtacagtctgaagcgcgctgactgcagggggggtgtcctgtgcagGTCTGTTTCCAAAGTCAATGCCTTCGTGGCTGATCACATTCTGGTCAGCAGTCGCCTTGCTTCTCGTGCTCTTTGTGTGGACGTGGAAATACCGAACAAT
                         cgctgac  putative branch site (score: 34)