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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgttttctgaattttgttgcccattttgttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA

Basic information

species Oryza sativa
transcript LOC_Os02g55410.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
gttaatcttcccatccaaaagtgaactg---ccaacttgtcaactttg---ttttctgaattttgttgcccattttgtt-----ccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA
|||| | ||  ||||| |  ||  ||      || ||  | ||| |||   ||| |||||     ||   |||||| ||     |  ||||||||| |||||||||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||||  |||||||||||||||||||||
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 17
gttaatcttcccatcc---------aaaagtgaactgccaacttgtcaactttgttttctgaattttgttgcccattttgttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA
||||  |||  |||||         |||| | |   |||  ||||  |  |  |||||||||||   |    ||||||| | || ||||||||| || ||||| |||||| |||| ||||| ||||||||||||||||| |||||||| ||||| |||| |||||| |||||||| ||||| |||||||
gttagcctttgcatccccagagtacaaaattcagtggcc--cttgaaatttgcgttttctgaat---gccctccattttatcccgacagCAAGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCA

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgttttctgaattttgttgc-ccattttgttcc---aacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA
|||  ||||   ||  |||  |  ||   |   || |   | |     |  | ||  |   |    | |||        | |||||||||||  | || ||||||||||| || || ||||||| ||||||||| ||  || | ||||| ||||| || |  || ||||||||||||||||| |
gtttgtcttgtgat--aaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 16
gttaatcttcccatccaaaagtgaactgcca-acttgtcaactttgttttctgaattttgttgcccattttgttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA
|||  ||||   ||  | |  |  || | |    |  || |  ||  | ||  |||    |     |  ||||   | |||||||||||  |||| ||||||||||| || |||||||||| ||||||||| ||  || | ||||| ||||| || |  || ||||||||||||||||| |
gtttgtcttgtgat--agacatagaccgtcttgttcatctagcttaatatcctaatggattactttacattgtg--agcagCAAGCTGAAACACAGATAAAGAGAAGAATTGGAATTGGAAACCACATATCGGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA

upper sequence: LOC_Os02g55410.1 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgt-tttctgaattttgttgcccattttgttcc-----aacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA----
            ||  | |     ||  |||  || ||   | | | ||||| | ||||  |  |  ||  |||||     |||||||||||||  |||| ||||||||||| ||||||||||||||||||||||| ||| |||| ||||| |||||  | |  |||||||| ||||||||||| |    
---------gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT

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|58687062|gb|CK075749.1|CK075749
EST:     CAGATATTGCAAATGAGATCAAG                         CAAGCTGAGGCACTAATTAAGAGAAGGATGGGAATTGGAAGCCACATATCC
genomic: CAGATATTGCAAATGAGATCAAGgttaatcttc ... gttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCC
EST: gi|86427693|gb|CI072790.1|CI072790
EST:     GAATCAATGAGCATTTGAACCTATCACCAGATATTGCAAATGAGATCAAG                         CAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTATCACCAGATATTGCAAATGAGATCAAGgttaatcttc ... gttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCC
EST: gi|58675180|gb|CK063867.1|CK063867
EST:     GAATCAATGAGCATTTGAACCTATCACCAGATATTGCAAATGAGATCAAG                         CAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCC
genomic: GAATCAATGAGCATTTGAACCTATCACCAGATATTGCAAATGAGATCAAGgttaatcttc ... gttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgccaacttgtcaactttgttttctgaattttgttgcccattttgttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA
                                         ttttgttcc  CT-rich tract
                           aattttgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatcttcccatccaaaagtgaactgccaacttgtcaactttgttttctgaattttgttgcccattttgttccaacagCAAGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG