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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccag

Basic information

species Oryza sativa
transcript LOC_Os05g29050.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G066485_T01 (Zea mays), 5'ss of exon 10
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttcc--attgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttt--tccag
|||||| ||||||||||||||||||||||||||||||||||| || |||||||| || ||||| || ||||||||||||||||||||||||||||||||||||  |  | |||   | |  | || |||||||           |     |||||  || |   |||||||  | |||
ATATCCCCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTATGGCCCACCTTGCCGTGATGTAGCGAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgttgcttatatccttgtggtctgcttatcatag-----------aaagcggtaaactaattgtttttttttctttcag

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA15G16270.1 (Glycine max), 5'ss of exon 11
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtctt---------ttccattgcatact-----catcatagtctt-ccccttcatt------attgtaaataaaataccttttttttccag---
||||||||| |||||||||||||||||||| ||||| || |  || |||||||| || ||  |||| ||||| ||||||||||| ||||||||||| |||||| |||||         || ||||| |  ||     |||  | ||| |   |||  |||      || | |||||| ||   |||| ||  ||    
ATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGGGGACCACCTTGCCGTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtcttattttgcagttgcattgaagtcttgaagcattctggtcctattcctatattcccaaaataggaaataatattttttttattaacatcag

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA09G04620.1 (Glycine max), 5'ss of exon 11
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtctt---------ttccattgcatact-----catcatagtcttccccttcattattgtaaataaaataccttttttttccag----------
||||||||| |||||||||||||||||||| ||||| || |  || |||||||| || ||  |||| ||||| ||||||||||| ||||||||||| |||||| |||||         || ||||| |  ||     |||  | ||| |   | |   |    ||||||  | |   | |||||              
ATATCCTCGTATGCCTTGGCATGATGTTCATTGTGCCCTTTGGGGACCACCTTGCCGTGACATTGCTAGGCACTTTGTTCAGCGATGGAATTATGCCAAGgttagtcttattttgcaattgcattgaagtcttggagcattctggtcctattcctatattccctaaataggaaataatattttttttattaacgtcag

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT3G16785.1 (Arabidopsis thaliana), 5'ss of exon 11
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcata-------gtcttccccttcattattgtaaataaaataccttttttttccag
  |||| || ||||||||||||||||| || |||||| | |  || |||||||| || ||||| || ||||| |||||||| |||||||| ||||| ||||||   |  | |   |  |   |  |  ||       || || ||  | ||||  ||||  | ||    | | |||| |||
GCATCCACGGATGCCTTGGCATGATGTGCATTGTGCTTTATGGGGACCACCTTGCCGTGATGTGGCTAGGCACTTTGTTCAACGCTGGAACTATGCTAAGgttcacccatacttctttaactttcttctatctgtttgtttttcctgttattaccgtaa-cataaccattgtgtttttcag

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 5'ss of exon 12
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccag----------------
||||||||| ||||| |||||||| || || ||||| || |  || || |||||||| ||||| || ||||| ||||||||||| ||||| ||||||||||||  | | ||| | | |||||||  | ||||  | |  ||||  | | |||  ||  |    | |   | ||                 
ATATCCTCGTATGCCATGGCATGACGTCCATTGTGCCCTATGGGGACCGCCTTGTCGTGATGTAGCTAGGCACTTTGTTCAGCGTTGGAACTATGCAAAGgttgatgtcttc-actacatactc--cctagttcttct-ttcaaaagtataataaaccttttatctcaatacaagcatacttttctgcag

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ21271 (Selaginella moellendorffii), 5'ss of exon 11
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcat--agtcttccccttcattattgtaaataaaataccttttttttccag
|   ||||||||||| ||||||||| ||||||||||  | |  |||||| ||||||||||||| ||| |||||||||| ||||| |||||||||||||||||  | |       || ||  ||  |  |  | | ||    |   || || | |                      
AACACCTCGCATGCCATGGCATGATATTCAGTGTGCAATATGGGGTCCAGCTTGTCGGGATGTCGCACGGCATTTTGTCCAGCGTTGGAATTATGCAAAGgtaaggcaccagtgttacaatctgtttctgaaattttgtagtgttttgttctcag---------------------

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ12042 (Selaginella moellendorffii), 5'ss of exon 11
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccag
|   ||||| ||||||||||||||| ||||||||||  | |  |||||| ||||||||||||| |||||||||||||| ||||| |||||||||||||||||  |           | |      | |   |||    ||  | | |||||           |||| || ||||
AACACCTCGTATGCCTTGGCATGATATTCAGTGTGCAATATGGGGTCCAGCTTGTCGGGATGTCGCAAGGCATTTTGTCCAGCGTTGGAATTATGCAAAGgtaag-----------ggaccagtgttaatatctgtttctgaaattttgtag--------tgttttgttcccag

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|58669537|gb|CK058223.1|CK058223
EST:     CTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAG                         AGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCAC
genomic: CTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttt ... ttttttccagAGGAACAAAGCTCCCAATGAGCAAGGAATTCCCTTGCTGATGCCTCATCAC




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCCTCGCATGCCTTGGCATGATGTTCAGTGTGCTCTCTACGGTCCACCTTGTCGGGATGTTGCAAGGCATTTTGTTCAGCGCTGGAATTATGCAAAGgtttgtcttttccattgcatactcatcatagtcttccccttcattattgtaaataaaataccttttttttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG