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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagacatatcatgattcaaagtttttaatcctctttgcaaacaataattactatatttcataagttccttctgttctcttttgaactttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCAGTGTATTACTCTGATGGGGATACATTGAAGGATCTGGCCCTTGAGCTTG

Basic information

species Oryza sativa
transcript LOC_Os02g32350.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G136296_T02 (Zea mays), 3'ss of exon 7
gtaagacatatcatgattcaaagtttttaatcctctttgcaaacaataattactatatttcataagtt--ccttctgttctcttttgaactttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCAGTGTATTACTCTGATGGGGATACATTGAAGGATCTGGCCCTTGAGCTTG
|||||   |||| |  |  ||  ||  |     |  |||     |||||||    | |||  | | ||  |||    ||  ||| | ||     | ||||||||| || ||||||||||||||||| || || || ||||||||||| || ||||||||| ||||||| || ||    |||||  |||||||||||||||
gtaagc--tatctttttctaatcttcctctaatttcttggtgtgaataatt----tgttttgtgacttggcctaacttttccttataaaaaaaaccctagGTGCGTATCGTGGTGGAAGGCACAGACAGCTTTAGTAATATAATTGGTTCTGTGTATTACCCTGATGGAGAGACTGCAAAGGACTTGGCCCTTGAGCTTG

upper sequence: LOC_Os02g32350.2 (Oryza sativa), 3'ss of exon 6
lower sequence: AC207890.3_FGT002 (Zea mays), 3'ss of exon 6
gtaagacatatcatgattcaaagtttttaatcctctttgcaaacaataattactatatttcataagttc-cttctgttctcttttgaactttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCAGTGTATTACTCTGATGGGGATACATTGAAGGATCTGGCCCTTGAGCTTG
|||||  || |  |  |   |  ||  |      | |||     |||||||    | |||  | | ||  | |   || || ||  ||      |||||||||| |||||||||||||||||||| || || || ||||||||||| || ||||||||| ||||||| || ||    |||||  |||||||||||||||
gtaagctatctgttattatgatcttcctctattcccttggtgtgaataatt----tgttttgttacttggcctaacttttccttataaaaaaattctagGTGCGTATTGTGGTGGAAGGCACAGACAGCTTTAGTAATATAATTGGTTCTGTGTATTACCCTGATGGAGAGACTGCAAAGGACTTGGCCCTTGAGCTTG
















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|29622118|gb|CB627129.1|CB627129
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|29674463|gb|CB670738.1|CB670738
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|29623577|gb|CB628588.1|CB628588
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|58607777|gb|CK035810.1|CK035810
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|58670976|gb|CK059662.1|CK059662
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAA
EST: gi|29625604|gb|CB630615.1|CB630615
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|29656202|gb|CB652477.1|CB652477
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|29644258|gb|CB649265.1|CB649265
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGGGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
EST: gi|29623984|gb|CB628995.1|CB628995
EST:     TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGAT                         GTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA
genomic: TTGGAATAGAAGCTAAGCACTTCACAGAGACACGGGTTCTCAATAGAGATgtaagacata ... tttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caataattactatatttcataagttccttctgttctcttttgaactttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCAGTGTATTACTCTGATGGGGATACATTGAAGGATCTGGCCCTTGAGCTTG
                       ttccttctgttctctt  CT-rich tract
     attactatatttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagacatatcatgattcaaagtttttaatcctctttgcaaacaataattactatatttcataagttccttctgttctcttttgaactttcctctagGTGCGAATTGTGGTGGAAGGCACAGATAGTTTCAGCAATATAATTGGCTCAGTGTATTACTCTGATGGGGATACATTGAAGGATCTGGCCCTTGAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT