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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctacatgcttccgcttccgcctatatgcatatgcattgcctgctatagtaccagctgtgtaatagtatgtacagttctgatggcctggcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGTTCCGGATCAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATG

Basic information

species Zea mays
transcript GRMZM5G879749_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g55130.4 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------------tctct-acatgcttccgcttccgcctatatgcata----tgc--attgcctgctatagtacc---agctgtgtaatagtatgta--cagttctgatggc-----ctggca--ctggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGTTCCGGATCAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATG
                                                           ||||| | |  ||   | |     |  | || ||     |||  |||  ||  || |||  |   ||||||  ||   |   ||   |  ||   |        |||  |   |  |||||||||||||||| ||| | ||||||||||| || || ||||| ||||| ||  |||| ||  ||||||||||||| || |  || ||||||||||||||
gtaaatagcaactgtaacatgaagatagcagtagtgcttactgttttactactagtatctctctgatagtctgatgttctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG

upper sequence: GRMZM5G879749_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 3'ss of exon 1
tctctacatgcttccgcttccgcctatatgcatatgcattgcctgctatagtaccagctgtgtaatagtatg--tacagttctgatggcctggcactggc-agGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGTTCCGGATCAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATG
   |||    |||  | ||       ||   || |        | || |||    ||     |  |  | |   | ||||  |  | ||     | |  | ||||||||||||||| ||| | ||||||||||| || || ||||| ||||| ||  |||| ||  ||||||||||||| || |  || ||||||||||||||
---ctaatcactttggattggattgctaattatcttttaaagttactgtagctgtagaaacatccttatttaactccagtaatatttgctgataatttcccagGTCCTGGATGCTCATCGATTGCGTATGGAGCATCTGAAGAGATTGGCCCATTTAGGATTAAGACAAACGGGACAGGGCTCTATCTGAACAAGTACTCATG
















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|94479697|gb|EB708655.1|EB708655
EST:     CTCTGGCTCAACGGAG                         GTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
genomic: CTCTGGCTCAACGGAGgttagtcagt ... gcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
EST: gi|91050418|gb|EB160836.1|EB160836
EST:     CACACCTTTCTCTGGCTCAACGGAG                         GTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
genomic: CACACCTTTCTCTGGCTCAACGGAGgttagtcagt ... gcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
EST: gi|101395266|gb|EB819563.1|EB819563
EST:     CTCTGGCTCAACGGAG                         GTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
genomic: CTCTGGCTCAACGGAGgttagtcagt ... gcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
EST: gi|71775053|gb|DR972931.1|DR972931
EST:     CTCTGGCTCAACGGAG                         GTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT
genomic: CTCTGGCTCAACGGAGgttagtcagt ... gcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatagtaccagctgtgtaatagtatgtacagttctgatggcctggcactggcagGTCCTGGATGCTCGTCGGTGGCGTATGGAGCGTCGGAGGAGATCGGCCCGTTCCGGATCAAACCAAACGGGACAGGCCTGTTCCTCAACAAGTACTCATG
                                ttctgat  putative branch site (score: 3)
                 taatagtat  TA-rich tract