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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC

Basic information

species Oryza sativa
transcript LOC_Os02g49230.5
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G167560_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------------ttagacatgtggatg-cttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
                                                                                        |  | | ||  |  |||| | ||||| |  ||  | |   || ||  |   | |||  | |  |  |       | |||||  ||||     |  |||| |||||||||||||| || ||||||||||| |||||||||||||| ||||| || |||||||| ||||||||| |||||||||||||||| |||||||| 
gtaagcacgtttaaatgtctgcttgaggttgttctgcgcttaacattcatagatcgtggctatctttttaaggcaaaaaaatgtctccaaccttctgtgtctcttgtttctagtttcgataatgc---attttccttgcagaagtcgctgattcacctttccttttcacgaatttgg---tcgacagGTTTGACAAGAAGATCAGATATGCTTCTCGCAAGGCTAGGGCAGACGTGAGGAAGAGGGTCAAGGGACGGTTTATAAAGGCTGGCGAAGCGTATGACTAT

upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G075562_T02 (Zea mays), 3'ss of exon 3
-------------------------------------------------ttagacatgtggatgcttgctcctagtgtgaatgct----actttatgtttttcttaaaagaagttattatatggcctt--tcttcacatattttcttc----------ttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
                                                 | | | |       |||  ||  |   |  |||||     || || ||  | |||       ||||   |||  |  ||   |||  | | | || | |             |||| |||||||||||||| || ||||||||||| ||||||||||| || ||||| ||  ||||||| ||||||||  ||||||| || ||||| || ||||| 
gtaagcacggctaaatgtctttttgtggttatttttctgcgcctaacattcatatagaccatggctatctttttaagcaaatgcctcccaccttctgggtctctcgtttctagttccaatactgtattgaccttttcttttcttttccacgaatttggccgacagGTTTGACAAGAAGATCAGATATGCTTCTCGCAAGGCTAGGGCGGACGTGAGGAAGCGGGTCAAGGGACGGTTCATAAAGGCCGGTGAAGCGTACGACTAT

upper sequence: LOC_Os02g49230.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv00s0194g00070.t01 (Vitis vinifera), 3'ss of exon 4
--ttagacatgtggatgcttgctcctagtgtgaatgctactttatgtttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
  | | | | | | | | ||  |       |  ||   | |  |  ||||  | |  | ||  || | | |   |||| ||||   | |  ||| | ||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| || ||  | || || || || ||||| ||||||||||| || ||||| |||
actaaaataagggtaggatttttatggaatttgattagaatgaaaattttcataactaaaaaataattttttttcttt-ttcat-caatgacttatgaacagATTTGAGAAGAAAATAAGATATGCCTCTCGCAAAGCAAGGGCAGATGTCAGGAAGCGTGTGAAGGGGCGATTTGTTAAGGCTGGCGATGCTTATGATTAC

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|700150|gb|D46441.1|D46441
EST:     AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGNAA                         ATTTGACAAGNAGGTAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
genomic: AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGAAAgtaagtgcat ... ttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
EST: gi|33815340|gb|CF333525.1|CF333525
EST:     AGCAGAGATAATGCTCTTACACGGTACAAGGAGGAGAAGAAGAGAAGAAA                         ATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG
genomic: AGCAGAGATAATGCTCTTACACGGTACAAGGAGAAGAAGAAGAGAAGAAAgtaagtgcat ... ttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttaaaagaagttattatatggcctttcttcacatattttcttcttaacagATTTGACAAGAAGATAAGGTATGCTTCTCGTAAGGCTAGGGCAGATGTGAGAAAAAGGGTCAAAGGACGGTTTGTAAAGGCTGGCGAAGCATATGACTAC
                          cctttcttcacatatt  CT-rich tract
     ttaaaagaagttatta  TA-rich tract