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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatacgtagttgaaactttgtcatgctgaatgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG

Basic information

species Oryza sativa
transcript LOC_Os04g58750.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
tatacgtagttgaaactttgtcatgctgaatga--tttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttg-ctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
   |||| | |  || |||| | |  |  |  |  |||     |||       |   | | | ||||| |   | ||||  | | | | || |||  ||||||||||| |||||||||||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||  || |||| ||||
---acgtggattgaaatttgacgttttctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttctgcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG

upper sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
tatacgtagttgaaactttgtcatgctgaa-tgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgct---gcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
|||   |  |   |  | | ||||  |||  || |||  ||   |  || | |  || |      |||| | ||||   ||  |||| || |    |   |||||| ||||| || |||||||| || || ||||| || |||||||||||||||||||| || |||  ||||||||| || ||||| ||     |||||||||
tatgtcttttcacatttgtatcatattgacctgtttttccatgtagactggctgaatgg----attgttccctgatttctttatttcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG

upper sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT4G00710.1 (Arabidopsis thaliana), 3'ss of exon 9
tatacgtagttgaaactttgtc---atgctgaatgatttagcaaccatcctcgttatattgttatgctgttg------catgatccattgttttccttgtttgc---tgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
  ||| |  |   || | |||    |   | | || ||| ||     |  ||  |  || |||    | |||      |||| |     |||    | |||||    |||||||||| ||||| ||||||||  | || ||||||||  | |||||||| ||||||||||||||    |||||  | ||||| |||||       || || |
-gtaccttttcagaattatgttggaagaatcagtggtttggctctgttaatcagtgaatagtttctttcttggttcttcatggtgttgcgttactttggtttggcaatgcagCTCTCGTTTCATATGTGGACAGACCAGATGCAAGAGTCTTTGAACTCGAAGAAGAAGGGTGATGTGGCTTTCAGGCAAAAAGACTTTAGAGAGGCCATCG

upper sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
--tatac-gtagttgaaactttgtca----tgctgaatgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
  || |  | |     | || ||||     || | |||| | ||| | |   |       |||    ||| | |||| | ||  |||||||| || | ||   |||||| ||||| |||||||||||||| || |||||||| ||||||||||||||||| ||||||||   |||||| || || || || ||     |||||||||
gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctata--catggtcttgc-taatt-attgtttttctagctt---gcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG

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|88720188|gb|CI743487.1|CI743487
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|88724708|gb|CI747967.1|CI747967
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|33796952|gb|CF324339.1|CF324339
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|33675770|gb|CF304009.1|CF304009
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|29636566|gb|CB641575.1|CB641575
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|88725714|gb|CI748973.1|CI748973
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|33679197|gb|CF307436.1|CF307436
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG
EST: gi|58603429|gb|CK013957.1|CK013957
EST:     AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAG                         CTCTCATTTCAGATGTGGACCAATCAAATGCCAGATACATTGAACTCCAAG
genomic: AAATCCTAGAAAAGACGGGCTACAAGGATGATGAGGGAACAGCAAATGAGgttttagttt ... tttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcgttatattgttatgctgttgcatgatccattgttttccttgtttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG
                                 ttgttttccttgttt  CT-rich tract
     ttatattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatacgtagttgaaactttgtcatgctgaatgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - catcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatga