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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccattatgtcagcattgcgattgactcaactgcactattttccgtgtactaacaaagaggtataagcacaaaatttgacacggttaatcacattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTCCCACAAGCGGTTCGCCACCGCGTTCCACAGCTACTGCAACCTCGTCGAC

Basic information

species Oryza sativa
transcript LOC_Os05g43300.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g43300.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G368410_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------tccattatgtcag-cattgcgattgactcaact---------gcact--attttccgtgtactaacaaagaggtataagcacaaa-atttg-acacggttaat-------cacattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTCCCACAAGCGGTTCGCCACCGCGTTCCACAGCTACTGCAACCTCGTCGAC
                                                  || |      ||| |||||| ||  | | | ||          || |  |  |  | | |  |   |||  |     |  |||   ||| |  |||   | |        || |||  ||||||||||||  |||| ||||||||||||||||||||||| |||||| |||| |||||||| || || || || ||| |||||||||||| ||||||||||
gtgcggatcgtagcttaatccataccaaaatcagccactgccactaacattctacccatccagacattgccatacattgagctctggttctcacattggaactgtcatatgttgggaaatggtgcctaatacatgcattcgtgcactactgaaagctttacaaatttgcagGAGAGCTGTAGTCACTGGGAGAGCAGTGAGGGTGAAGTCGCAGCTGCAGTCTCACAAGCGATTTGCTACGGCTTTCAACAGCTACTGCAGCCTCGTCGAC
















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|218505355|gb|FG968511.1|FG968511
EST:     CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAG                         GAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC
genomic: CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAGgtatgcttca ... acattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC
EST: gi|88353182|gb|CI654448.1|CI654448
EST:     CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAG                         GAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC
genomic: CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAGgtatgcttca ... acattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC
EST: gi|88344019|gb|CI638754.1|CI638754
EST:     CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAG                         GAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTG
genomic: CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAGgtatgcttca ... acattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTG
EST: gi|29682841|gb|CB679116.1|CB679116
EST:     TCAGGGGAATCAG                         GAGAGCTGTGATCACC-GGACGAGCAGTGAGGGTGAAGTCCCAGCTGAAGT
genomic: TCAGGGGAATCAGgtatgcttca ... acattgtcagGAGAGCTGTGATCACCGGGA-GAGCAGTGAGGGTGAAGTCCCAGCTGAAGT
EST: gi|29624215|gb|CB629226.1|CB629226
EST:     CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAG                         GAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC
genomic: CTCGTAGGTGTGGTCTGTGATGCCTATCTTGCGGTTGTCAGGGGAATCAGgtatgcttca ... acattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtactaacaaagaggtataagcacaaaatttgacacggttaatcacattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTCCCACAAGCGGTTCGCCACCGCGTTCCACAGCTACTGCAACCTCGTCGAC
                       acaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccattatgtcagcattgcgattgactcaactgcactattttccgtgtactaacaaagaggtataagcacaaaatttgacacggttaatcacattgtcagGAGAGCTGTGATCACCGGGAGAGCAGTGAGGGTGAAGTCCCAGCTGAAGTCCCACAAGCGGTTCGCCACCGCGTTCCACAGCTACTGCAACCTCGTCGAC

- - - - - - gcattgc
- - - - - - - - - - - - - - aactgca
- - - - - - - - - - - - - - - - - - - - - ccgtgta
- - - - - - - - - - - - - - - - - - - - - - - - - taacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcacaaa