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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatataatgcattctttcttttttttgagagaactacactgcattcgttatttgtaactcgatcaacgttaggtgctcagcaaaatgatcacttttgctcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTATGACAAAGAAGGAAGCCCATACTACTCCACCGCTAGACTTTGGGACGATG

Basic information

species Oryza sativa
transcript LOC_Os08g32850.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g32850.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G702490_T02 (Zea mays), 3'ss of exon 10
gtatataatgcattctttcttttttttgagaga-actacactgcattcgttatttgtaactcga---tcaacgttaggtgctca-gcaaaatga---------tcacttttgctcttacgca-----gTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTATGACAAAGAAGGAAGCCCATACTACTCCACCGCTAGACTTTGGGACGATG
|||||| |||| ||| | ||| | | |||| || || | | || | || |||| | | || || | || || |||| | ||| || ||||| ||| || |||||||||||||||||||| ||||| ||||||||||| |||| |||||||||||| ||||||||||| ||||| || |||||||| |
gtatatggatcattaattccgtgtttcagaaaacactaaacagcgtgactcgttgaaggtttgaatgtcaaaacgacttccttttacatgacgaattcgaacctctttttttttgttatacaatacagTGGAGCAAGGACGAGGAAGAAGCCTTCAAAGCCAAAGTCGTGGAGGCTTACGACAGAGAAGGAAGCCCGTACTACTCCACTGCTAGGCTATGGGACGACG
















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|88414102|gb|CI533472.1|CI533472
EST:     GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|89194521|gb|CI116958.1|CI116958
EST:     GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|88831277|gb|CI082087.1|CI082087
EST:     CTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: CTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|29640037|gb|CB645046.1|CB645046
EST:     GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|29640075|gb|CB645084.1|CB645084
EST:     GTGTCCTTGCTCAAATAGAGAAGAACACCAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|31818575|gb|CD645562.1|CD645562
EST:     GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
EST: gi|29639362|gb|CB644371.1|CB644371
EST:     GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAG                         TGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT
genomic: GTGTCCTTGCTCAAATAGAGAAGAACAACAGAAAAAGACAAGGAGTGGAGgtatataatg ... tcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaactcgatcaacgttaggtgctcagcaaaatgatcacttttgctcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTATGACAAAGAAGGAAGCCCATACTACTCCACCGCTAGACTTTGGGACGATG
                                   tcacttttgctctt  CT-rich tract
 aaaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataatgcattctttcttttttttgagagaactacactgcattcgttatttgtaactcgatcaacgttaggtgctcagcaaaatgatcacttttgctcttacgcagTGGACCAAAGATGAGGAAGAAGCCTTCAAAGCAAAAGTTGTGGAGGCTTATGACAAAGAAGGAAGCCCATACTACTCCACCGCTAGACTTTGGGACGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA