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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttctttcttcacttataatacatttattaaatacacttagtcgcatgtattctatttgaattgaatcctgagtaatgttttccatcatggtaaaagTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACACTGAGGCGCACAACAGTAGTCTTTACAATGACAATGGAGTATTTCTTGG

Basic information

species Oryza sativa
transcript LOC_Os02g40030.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G133226_T04 (Zea mays), 3'ss of exon 3
gtatgcttctttcttcacttataatacatttattaaatacacttagtcgcatgtatt-ctatttgaattgaatcctgagtaatgttt-----tccatcatggtaaaa-gTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACACTGAGGCGCACAACAGTAGTCTTTACAATGACAATGGAGTATTTCTTGG----
|||||||  |  | | || || | ||    | |     | | |||| | |||| ||| || ||    |||||| |||| |  |||||     ||  |  |||||||| | |||||||||||||||| || |||||||| |||||||| ||||||||||| ||  ||||||| ||||| || |||||||||||||||||||||||| |||    
gtatgctgatccccttacatacagtattagtgtgtttaataattaggctcatgcatttctgttcatgttgaattctgattggtgtttactgttcttttttggtaaaaagctagCTTCAATGGAATCGGTCCGTGGAGTTAATGTTCCTATGTATACAACTCTACGGCGCACGACAGTTGTGTTTACAATGACAATGGAGTATTTCCTGGCAAA

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 3
gtatgcttctttcttcacttataatacatttattaaatacacttagtcgcatgtattctatttgaattgaatcctgagtaatgttttccatcatggtaaa-agTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACACTGAGGCGCACAACAGTAGTCTTTACAATGACAATGGAGTATTTCTTGG
|||||||   | | | || || || |    | ||    | | |||| | | || |||                     || |||| |   |  ||||||| || ||||||| |||||||| || |||||||| || ||||| ||||||||||| ||  | ||||||||||| || |||||||||||||||||||||||| |||
gtatgctgactcccttacatagaagattaatgtttttaataattaggcacttgcatt---------------------tactgttctttctt-tggtaaatagCTAGCTTCGATGGAATCGGTCCGTGGAGTTAACGTTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGG

upper sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G133226_T03 (Zea mays), 3'ss of exon 3
gtatgcttctttcttcacttataatacatttattaaatacacttagtcgcatgtatt-ctatttgaattgaatcctgagtaatgttt-----tccatcatggtaaaa-gTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACACTGAGGCGCACAACAGTAGTCTTTACAATGACAATGGAGTATTTCTTGG
|||||||  |  | | || || | ||    | |     | | |||| | |||| ||| || ||    |||||| |||| |  |||||     ||  |  |||||||| | |||||||||||||||| || |||||||| |||||||| ||||||||||| ||  ||||||| ||||| || |||||||||||||||||||||||| |||
gtatgctgatccccttacatacagtattagtgtgtttaataattaggctcatgcatttctgttcatgttgaattctgattggtgtttactgttcttttttggtaaaaagCTAGCTTCAATGGAATCGGTCCGTGGAGTTAATGTTCCTATGTATACAACTCTACGGCGCACGACAGTTGTGTTTACAATGACAATGGAGTATTTCCTGG

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|88422800|gb|CI573962.1|CI573962
EST:     GAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATG                         TTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA
genomic: GAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATGgtatgcttct ... atggtaaaagTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA
EST: gi|58667565|gb|CK056251.1|CK056251
EST:     GAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATG                         TTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA
genomic: GAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATGgtatgcttct ... atggtaaaagTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA
EST: gi|88422801|gb|CI573963.1|CI573963
EST:     GAATACTGTTGCGTACTACACCTCTTTATTTGGCTTATTTACTCTATATG                         TTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA
genomic: GAATACTGTTGCGTACTACACCTCTTTCTTTGGCTTATTTACTCTATATGgtatgcttct ... atggtaaaagTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcatgtattctatttgaattgaatcctgagtaatgttttccatcatggtaaaagTTAGCTTCAATGGAATCTGTGCGTGGAGTCAATGTTCCGATGTATACAACACTGAGGCGCACAACAGTAGTCTTTACAATGACAATGGAGTATTTCTTGG
      tattctatttgaatt  TA-rich tract