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'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttctgcctaacaaatatatttggcttcgctaatgcttgattgttttaaaatatgaaacagctcgttattttcccgttatgccctacaacttgacatctgcgttttttag

Basic information

species Zea mays
transcript GRMZM2G070045_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070045_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os02g51430.1 (Oryza sativa), 5'ss of exon 23
GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttctgcctaacaaatatatttggcttcgctaatgcttgattgttttaaaatatgaaacagctcgttattttcccgttatgccctacaacttgacatctgcgttttttag
|||||||||||| ||| | |||||||| ||||||||||||||| ||||||| |||||||||||||| || ||||| |||||||||||||| ||||||||||||||||| |    |||||   || | |  || || |    ||  | ||||          |  ||  | ||  ||||   | |||  ||  ||||||| |||| |||| | |||
GCGGATTCTGGCTGATCTAAGGGAGCTTGCTTCAGCTGAGAGTCTGGATAGTTTTACTCTCATTTATACAAATATTCTGGAACATCAACCAGATTGCCCGgtaatttttt---caacaagc-tactcgattttgccagaaattagtggttt----------agtagtgcattcatttctgttgatgtgctg-aacttgatatctacgttatgtag

upper sequence: GRMZM2G070045_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA03G03120.2 (Glycine max), 5'ss of exon 24
GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttctgcctaa-caaatatatttggcttcgctaatgcttgattgttttaaaatatgaaacagctcgttattttcccgttatgccctacaacttgacatctgcgttttttag
| |  | ||    ||  |||||||||| |||||||| |||||  |||||| |||||| ||||| || || |||||||| |||||||||||||| ||||||||||  || |||| || | ||| |   |   | |  | |    ||  ||| | |     | || ||| |      |||   |   ||   | ||| ||                  
GAGTGTACTTAGCGACTTGAGGGAGCTTGCTTCAGCAGAGAGCCTGGATACCTTTACACTCATCTATACAAATATACTCGAACATCAACCTGACTGCCCGgtaaaattatgcccaatctaatctcaatttttgcattcacaaatgcatgtatgagttctttaagcagttgaaatattttttgcagtgggtttcaagttat----------------
















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|44901257|gb|CK827802.1|CK827802
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|67012338|gb|CO441087.1|CO441087
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|60398228|gb|DN231044.1|DN231044
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|9733553|gb|BE512185.1|BE512185
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTTTTTATAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|108953640|gb|EC364817.1|EC364817
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|37375400|gb|CF624134.1|CF624134
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|67019171|gb|CO447920.1|CO447920
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|67016798|gb|CO445547.1|CO445547
EST:     GCCTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|56691655|gb|CX129558.1|CX129558
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
EST: gi|24934258|gb|CA452476.1|CA452476
EST:     GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCG                         CCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG
genomic: GCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAG

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: 27 (upstream exon), 49 (downstream exon)
Score: 163

GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAGGAAGCGAAGGAG


Block sizes: 27 (upstream exon), 47 (downstream exon)
Score: 185

GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAGGAAGCGAAGGAG


Block sizes: 27 (upstream exon), 47 (downstream exon)
Score: 147

GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAGGAAGCGAAGGAG


Block sizes: 27 (upstream exon), 45 (downstream exon)
Score: 124

GCGGATTCTGGCAGATATGAGGGAGCTAGCTTCAGCTGAGAGTTTGGATAGCTTTACTCTCATTTACACTAATATACTGGAACATCAACCTGATTGCCCGgtaattttct ... cgttttttagCCTGAGGTTGTCGAGAAGCTTGTGGCAATGCGGGAAGGCATTCCAAAAAAGGAAGCGAAGGAG