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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaatatctgaagccagaagttatcttttttgcccttattttactgcatagtggataaggctgaaaagctctattatag

Basic information

species Zea mays
transcript GRMZM2G171400_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171400_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g01620.1 (Oryza sativa), 5'ss of exon 2
TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaatatctgaagccagaagttatc--ttttttgcccttattttactgcatagtggataaggctgaaaa---gctctattatag
|||||||||||||| ||||||  || ||||||||| ||| |||||||||||||| ||||| ||||||||||||||| | ||||| |||||||| ||||||||||||||| |||||||||||  |  ||||  ||||||||||||||||| |||| |||||||||||||||||||      |||||||||
TTGTGGAGATGACAGCCAGGGCGTTTTGTTTGTCAGCAACATGAGCTTTAGTGGAGTAGACCTCACAAGATTAAGGACAAAAAAGGGGCACACTGCTCAGgtagtctaaaatctgaagccaatatctatctattttttgcccttattttgctgcttagtggataaggctgaaaataatacctattatag
















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|148949091|gb|EC894518.2|EC894518
EST:     GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
genomic: GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
EST: gi|211081204|gb|FL350812.1|FL350812
EST:     GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAA-GGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
genomic: GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
EST: gi|71449339|gb|DR830389.1|DR830389
EST:     GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
genomic: GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
EST: gi|91877865|gb|EB407822.1|EB407822
EST:     GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCANGCGGCAATCGCACCATGCGGCCATGCCTA
genomic: GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
EST: gi|211474900|gb|FL324941.1|FL324941
EST:     TGGGTGTAGATCTCACAAGATTAAGGGCGGAAAAAGGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCAAGCGGCA
genomic: TGG-TGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCA
EST: gi|9028606|gb|BE238646.1|BE238646
EST:     GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAG                         TGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA
genomic: GTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTA

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: 46 (upstream exon), 47 (downstream exon)
Score: 157

TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTATCTAGTGCAGTCAAGATACAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 59

TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTATCTAGTGCAGTCAAGATACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 75

TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTATCTAGTGCAGTCAAGATACAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 88

TTGTGGAGATGACAACCAGGGACTTCTGTTTGTCAACAATATGAGCTTTAGTGGTGTAGATCTCACAAGATTAAGGGCGAAAAAAGGGCACACCGCTCAGgtagtctaat ... tctattatagTGTGTGTGCTTGGTCGATGCAAGCGGCAATCGCACCATGCGGCCATGCCTATCTAGTGCAGTCAAGATACAG