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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatctgtcagcgccattttctctctttaatctgcacctttagcatgcaaaatgttgcaatcttcctctttgttaaacatcaacacgttttgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g02020.3
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.2 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM5G860137_T02 (Zea mays), 3'ss of exon 11
ttatctgtcagcgccattttctctctttaatctgcacctttagcatgcaaaatgttgcaatcttcctctt-tgttaaacatcaacacgtttt--gctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT
|||| | |  | | |||  | |||    ||||| ||  ||||| |        | ||||    |  | |  || ||| | || |    || |  | ||  |||||||||||||| |||||||||||  |||| |||||||||||||||||||| || || || ||||| ||||| ||| |||| |||||
ttatattttggtgtcatgctttctg---aatctccatgtttagtagtactttggatgcatcggtgttgtagtgctaatcttctagcttttctctggtcagcagATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCAT
















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|88449714|gb|CI539089.1|CI539089
EST:     TTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: TTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|86886429|gb|CI336132.1|CI336132
EST:     GCCATCCTATTGGTTCCACTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88470166|gb|CI407437.1|CI407437
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88261356|gb|CI364932.1|CI364932
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|125863427|gb|EL586709.1|EL586709
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88457931|gb|CI542113.1|CI542113
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|89191076|gb|CI392929.1|CI392929
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|86600622|gb|CI356379.1|CI356379
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88276828|gb|CI395991.1|CI395991
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|22306530|gb|BQ907752.1|BQ907752
EST:     CATCCTATT-GTT-CAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATT-GGGTTGCTGGAGTTTGCAATGGA
genomic: CATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|86868992|gb|CI334364.1|CI334364
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88272428|gb|CI386283.1|CI386283
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTC-GG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88322667|gb|CI542995.1|CI542995
EST:     AGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: AGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|89194176|gb|CI116613.1|CI116613
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|86494598|gb|CI137231.1|CI137231
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGA
EST: gi|88260275|gb|CI362568.1|CI362568
EST:     GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGG                         ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGGTTTGCAATGG
genomic: GCCATCCTATTGGTTGCAGTGGTGCGAGAATCATAGTCACTTTGCTCGGGgtatgctacc ... tgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGA-GTTTGCAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaaatgttgcaatcttcctctttgttaaacatcaacacgttttgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT
                                          ttttgctcc  CT-rich tract
                       tttgttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatctgtcagcgccattttctctctttaatctgcacctttagcatgcaaaatgttgcaatcttcctctttgttaaacatcaacacgttttgctccacagATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG