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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatttgtccttgctgcacatagtatgcaaaatctgtaacactgagtcactgaccaacagtgaaacgggacaaaaatttcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os06g49990.2
intron # 14
splice site 3'
intron type U2

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|218783416|gb|GE329468.1|GE329468
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCT
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCT
EST: gi|27578134|gb|CB000829.1|CB000829
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88508220|gb|CI435726.1|CI435726
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88566864|gb|CI497581.1|CI497581
EST:     TTTCAATC-TCAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: TTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|33687914|gb|CF316153.1|CF316153
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|86834903|gb|CI345987.1|CI345987
EST:     GTCATGAAAAATGGATATATTGCAAATGTTACCCTCTTTCAATCATGAG                         TGCTAACACCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|27577736|gb|CB000431.1|CB000431
EST:     GGCATGAAAAATGGATCTTTTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88427508|gb|CI548761.1|CI548761
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88469123|gb|CI406394.1|CI406394
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATNGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88504066|gb|CI431572.1|CI431572
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCACCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88249403|gb|CI249252.1|CI249252
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88565703|gb|CI496420.1|CI496420
EST:     TTTCAATC-TCAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: TTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|33687915|gb|CF316154.1|CF316154
EST:     GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: GTCATGAAAAATGGATATATTGCAACTGTTACCCTCTTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
EST: gi|88565726|gb|CI496443.1|CI496443
EST:     TTTCAATC-TCAG                         TGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA
genomic: TTTCAATCATGAGgtatgtattt ... tcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtaacactgagtcactgaccaacagtgaaacgggacaaaaatttcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG
              cactgac  putative branch site (score: 2)
                                    acaaaaatttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtatttgtccttgctgcacatagtatgcaaaatctgtaacactgagtcactgaccaacagtgaaacgggacaaaaatttcaatctcagTGCTAACAGCTGATGGTGATGCATATCCAGCCGCATCTGCATTAATGGTTAGACAGTGCTGCTACTCCAAATGGGACTCTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT