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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtatcaaacaagaaactttaaggcaattgtcaaagataattaattctgtattccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA

Basic information

species Zea mays
transcript GRMZM2G092588_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g33580.1 (Oryza sativa), 3'ss of exon 6
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataat-taattctgtattccactttt---ttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
||| ||||||  |||||||     ||     | |||      || | |||   |  ||    |||   ||||| |||| |||||| | ||    |    |||||  |  ||||||||||||||| ||||| || |||||||| ||||||||||||||||||||||| || || ||||| || |||||||| ||||| |||||||| || ||||||
gtatgtatcactcaagaaaaac--agtgtgctctcaggttccatatcatttcatcatctgtgtttaccttttggtgatcactgatccagctgcctttcttttgtgctactttcagGTACAAGGTATTCATCAACCCGAGCATCAGTGATGTCCTGTGCACAGCAACAGCGGAAGCTCTCGCGATGGGGAAGTTCGTCATCTGCGCGGAGCATCCA

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G36050.1 (Glycine max), 3'ss of exon 6
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataa--ttaattctgtattccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
         | ||| ||  ||||       ||  ||     |   | |||   | |||    ||| ||  |||   | || ||  || ||       ||| |  || ||  |||||||| || || |||||||| |||||||||||||| || |||||||| || || ||||| ||||| ||||| ||||| ||  | || || || ||||||
---------acacatgattctttctcatcctttacatgcccagactcaatctggaatttgtttttattaagtttggttcttattttgacacac----tttatccttattgtagGTACAAAGTCTTTATAAATCCTAGCATTAGTGATGTGCTATGCACAGCTACAGCTGAGGCGCTTGCCATGGGCAAATTTGTAGTTTGTGCTGATCATCCA

upper sequence: GRMZM2G092588_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G11670.1 (Arabidopsis thaliana), 3'ss of exon 6
gtacgtatcaaacaagaaactttaaggcaattgtcaaagataattaattctgtattccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
                         |  | || | ||| ||      | || |     |||| ||   |||     ||     || | ||| |    |    ||  |  |||||||| || |||||||| || ||||| || ||||| || ||||||||||| ||||| || || || |||||||| || ||| | || ||||| || || 
-------------------------gtaagttctgaaaaatgtgctttgcttttaaaaacttgttaaggtttcgctctttgattgtc-tttcccacat---cttgatgaagGTACAAAGTGTTCATAAACCCCAGCATCAGCGATGTTCTATGCACAGCAACCGCAGAAGCACTAGCCATGGGGAAGTTTGTGGTGTGTGCAGATCACCCT

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|71427681|gb|DR808731.1|DR808731
EST:     AGTCTCAATTTTTTCAAGGGAAGGGATCATGCTGATAATTCACTCCATGG                         GTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAAC
genomic: AGTCTCAATTTTTTCAAGGGAAGGGATCATGCTGATAATTCACTCCATGGgtacgtatca ... tttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAAC
EST: gi|47961892|gb|CN844601.1|CN844601
EST:     AGTCTCAATTTTTTCAAGGGAAGGGATCATGCTGATAATTCACTCCATGG                         GTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAAC
genomic: AGTCTCAATTTTTTCAAGGGAAGGGATCATGCTGATAATTCACTCCATGGgtacgtatca ... tttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacttttttttgttgattactgatgctgccatttgctgtttgtatttttttcagGTACAAGGTTTTCATAAATCCGAGCATTAGTGATGTCCTGTGCACAGCAACGGCAGAGGCTCTTGCAATGGGGAAATTCGTGATCTGCGCAGAACATCCA
                  tactgat  putative branch site (score: 2)
                                       tttgtatttttttc  putative PPT
     tttttttgttgatta  TA-rich tract