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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttgctatttctcctatgcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA

Basic information

species Oryza sativa
transcript LOC_Os05g38370.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G035922_T02 (Zea mays), 3'ss of exon 3
gtctgttgctatttctcctatg--cgatgcaaatttgagttcctggtgtcta-taattgaatcag-ctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA
||  ||| || |  | |||||   ||| |       ||||| |     | ||  |||    | |  |||||| | || |||||||| || ||||||||||||||| |||| ||||| ||||| ||||||||||||||| | || ||||| ||||||||||||||||| || ||
gtgagttcctctaccacctatcttcgaagtggtaacgagtttccccaatttaacaatgtcgttattctttgtgtatgtagTGCAACCCTTATTTTTGAGGTGGAGCTAGTAGCTTGCAGGCCGAGGAAAGGTTCAAGCTTAGGTAGTGTATCTGATGAGAAAGCCAGACTTGA

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

upper sequence: LOC_Os05g38370.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv13s0019g01900.t01 (Vitis vinifera), 3'ss of exon 4
--gtctgttgctatttctcctatgcgatgcaaatt---------tgagttcctggtgtctataa--------ttgaatcagctttgtcttt-----gcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA
  ||    |  ||||| |  ||   | | || ||          ||  | |||  | |||| ||           | || ||| | |   |     |||||||||| ||  |||||||||||||||| || || || ||||| ||||| ||||||||| |  | ||||||||||||||||  || ||||| ||
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|25044727|gb|AJ420710.1|AJ420710
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88204275|gb|CI204124.1|CI204124
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88209738|gb|CI209587.1|CI209587
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|14571477|gb|BI118845.1|BI118845
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88836064|gb|CI371169.1|CI371169
EST:     CCAGAATACCCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTA-GAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|38477260|gb|CF961393.1|CF961393
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGG
EST: gi|109711641|gb|CI013246.1|CI013246
EST:     ATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: ATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCACCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|86417638|gb|CI031847.1|CI031847
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
EST: gi|88980703|gb|CI022414.1|CI022414
EST:     CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAA                         TGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG
genomic: CCAGAATACGCATACGGAAGTGCAGGGTCGCCGCCAGAGATTCCACCCAAgtctgttgct ... gtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgatgcaaatttgagttcctggtgtctataattgaatcagctttgtctttgcagTGCAACACTCATTTTTGAGGTGGAGTTAGTGGCTTGTAGGCCTAGGAAAGGTTCAAGCCTGGGCAGTGTTTCTGATGAGAAAGCCAGGCTAGA
                                         ctttgtcttt  CT-rich tract
                           tataattgaat  TA-rich tract