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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAGTAAGAT

Basic information

species Oryza sativa
transcript LOC_Os05g38370.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 3
gtctgttgctatttctcctatg--cgatgcaaatttgagttcctggtgtcta-taattgaatcag-ctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAGTAAGAT
||  ||| || |  | |||||   ||| |       ||||| |     | ||  |||    | |  |||||| | || |||||||| || ||||||||||||||| |||| ||||| ||||| ||||||||||||||| | || ||||| ||||||||||||||||| || ||       
gtgagttcctctaccacctatcttcgaagtggtaacgagtttccccaatttaacaatgtcgttattctttgtgtatgtagTGCAACCCTTATTTTTGAGGTGGAGCTAGTAGCTTGCAGGCCGAGGAAAGGTTCAAGCTTAGGTAGTGTATCTGATGAGAAAGCCAGACTTGA-------

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G55520.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------gtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAGTAAGAT
                   | ||||   |  | | | |   ||  |   |   ||  | || | | |||||||      || ||  ||||||||||||  | ||||| |||||||| || || |||||||| || ||||||||| | ||  | || ||||||||||| |||| ||||||||||||       
gtatgttatgttccaaacttcttgcatctcgttcaagggagtgtgacagttttttttttgtttttgtaattgagatt-tttggtaattgcagTGCAACTTTGATTTTCGAGGTGGAATTGGTTGCTTGTAGACCGAGGAAAGGTGCTAGTGTTGGAAGTGTTTCTGAAGAGAGAGCCAGGCTAGA-------

upper sequence: LOC_Os05g38370.2 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 4
--gtctgttgctatttctcctatgcgatgcaaatt---------tgagttcctggtgtctataa--------ttgaatcagctttgtcttt-----gcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAGTAAGAT
  ||    |  ||||| |  ||   | | || ||          ||  | |||  | |||| ||           | || ||| | |   |     |||||||||| ||  |||||||||||||||| || || || ||||| ||||| ||||||||| |  | ||||||||||||||||  || ||||| ||       
ttgttctatcttatttattttagtagttacagatcgatgacttgtggctcccttatttctaaaaactgaaagccaagtctgctgtattcatttaatgcagTGCAACCCTTGTTTTTGAGGTGGAGTTGGTAGCCTGCAGGCCAAGGAAGGGTTCAAGCATCAGTAGTGTTTCTGATGAGAGGGCTAGGCTTGA-------

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|88411482|gb|CI519006.1|CI519006
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGAGTAAGAT
                                         ctttgtcttt  CT-rich tract
                           tataattgaat  TA-rich tract