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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctggatatgtctttgtgcttttttttgttaggaaaaaatcttctttggttcatctatactcgaccttatcatatgttccatttctagggtatcttgctacctgccctttgcaatgttaagtttttgtatattggttataactgaccatttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTACGACATATGGATGTTTACGCCCACCCCTTGGAAAACATCGTTTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g40340.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g40340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G470292_T01 (Zea mays), 3'ss of exon 10
gtgagttctggatatgtctt-tgtgcttttttttgttaggaaaaaatcttctttggttcat-------------ctatactcgaccttatcatatgttccatttctagggtatcttgctacctgccctttgcaatgttaagtt--tttgtatattggttataactgac-catttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTACGACATATGGATGTTTACGCCCACCCCTTGGAAAACATCGTTTGAAG--
||||||  | ||||| || |   |  || |||   ||  || |   |  |   |  ||  |               |||    | ||| |   ||          |||       |||||       |||  |||  ||  ||  ||  | |||||||| | ||||||  |  |||  |||||| |||||||| |||||||| || || | |||||||| ||| ||||| || || ||||||||||| |||||||| ||||||||||||||| |||||  
gtgagtgttagatatttcatgcatatttatttcatttgcgacatcttgcttcataatttgtaagacttaggaaatcatatgttatcttgtttcataactgggccttagaaatgtatgctagacaatgtttcaaattctatattcgttgatttattggtt-tgactgacataagttttcagGCAACTTGCTGAATTTATTGGACACATCGGCTGCTGAAAGTGTGTTGCCAACAACTTATGGATGTTTGCGCCCACCTCTTGGAAAACATCGTCTGAAGGT

upper sequence: LOC_Os01g40340.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 1
gtgagttctggatatgtctttgtgcttttttttgttaggaaaaaatcttctt--tggttcatctatactcgacctt-----atcatatgttccatttct-----------------agggtatcttgctacctgccctttgcaatgttaagtttttgtatattggtt---ataactgac-catttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTACGACATATGGATGTTTACGCCCACCCCTTGGAAAACATCGTTTGAAG
||||||  ||||||| |   ||    ||| |||| |  |||  |   | |||  |  || ||      | |  |||     || ||||| | | || ||                 ||       ||||     ||  ||   ||  ||  | |||||  |||  ||   || ||||||  |  ||| ||||||| |||||||||||| |||| ||||| | | ||||||  |  ||||| || || ||||||| ||| |||||||| ||||||||||||||| |||||
gtgagtgttggatat-ttcatgcatatttatttggtttgaagcatcttgcttcataatttataggccttaggacttgggaaattatatgctaccttgcttcataattggtgggcttagaaatatatgctggacaccgattcttattctatatatttgttgatttattggtatgactgacataagtttttagGCAACTTGCTGAAGTTACTGGACACTTCGGCTACTGAAAGCGGGTTGCCAACAACTTATGGATCTTTGCGCCCACCTCTTGGAAAACATCGTCTGAAG
















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|58693869|gb|CK082556.1|CK082556
EST:     GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAG                         GCAATTTGCTGAAGTTATTGGATACTTCTGGTGCTGAAAATGTTTTGCCTA
genomic: GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAGgtgagttctg ... atttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA
EST: gi|29612947|gb|CB617960.1|CB617960
EST:     GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAG                         GCAATTTGCTGAAGTTATTGGATACTTCTGGTGCTGAAAATGTTTTGCCTA
genomic: GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAGgtgagttctg ... atttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA
EST: gi|58672704|gb|CK061390.1|CK061390
EST:     GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAG                         GCAATTTGCTGAAGTTATTGGATACTTCTGGTGCTGAAAATGTTTTGCCTA
genomic: GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAGgtgagttctg ... atttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA
EST: gi|58689270|gb|CK077957.1|CK077957
EST:     GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAG                         GCAATTTGCTGAAGTTATTGGATACTTCTGGTGCTGAAAATGTTTTGCCTA
genomic: GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAGgtgagttctg ... atttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA
EST: gi|29669991|gb|CB666266.1|CB666266
EST:     GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAG                         GCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA
genomic: GTTGGTCACTGCCAGTCCAGAGACTGTTGATGGCATGCTTGAGAGCCTAGgtgagttctg ... atttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccctttgcaatgttaagtttttgtatattggttataactgaccatttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTACGACATATGGATGTTTACGCCCACCCCTTGGAAAACATCGTTTGAAG
                                     aactgac  putative branch site (score: 2)
                                           ccattttt  CT-rich tract
          aatgttaagtttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctggatatgtctttgtgcttttttttgttaggaaaaaatcttctttggttcatctatactcgaccttatcatatgttccatttctagggtatcttgctacctgccctttgcaatgttaagtttttgtatattggttataactgaccatttttgtagGCAATTTGCTGAAGTTATTGGATACTTCTGATGCTGAAAATGTTTTGCCTACGACATATGGATGTTTACGCCCACCCCTTGGAAAACATCGTTTGAAG

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