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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttttatgttatatcttgcggtggttggtgttgggggagggtttatgtatagagaaattcgatattttttaaatgtttgtgattgattttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG

Basic information

species Oryza sativa
transcript LOC_Os05g06430.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G159369_T01 (Zea mays), 3'ss of exon 1
ggcttttatgttatatcttgcgg-tggttggtgttgggggagggtttatgtatagagaaattcgatattttttaaa-tgtttgtgattgattt-tgttt-tcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG
  || | |    | |||       |||      ||    ||   ||| | | ||| ||  ||   ||||  |||   | ||| ||| |   || ||||| | |||||||| |||||||| ||||||||||| || || |||||||| || || || |||||||| || ||||| || || || || |||
--ctgtgagcacaaatcacttatctggaaacctttctatgaccatttgt-tttagtgatctttt-tattggttactctttttctgactatcttctgtttcttagGTGTGGCCACTGCAAAAAGCTTGCCCCCGAGTATGAAAAACTTGGCGCCAGCTTCAAGAAGGCTAAATCTGTACTGATAGCAAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 2
-ggcttttatgttatatcttgcggtggttggtgttgggggagggtttatgtatagagaaattcgatattttttaaatgtttgtgattgattttgtttt--cagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG
   |   |   || ||        |  || ||  |        |||  | | |  |  |||  |  ||| | |  | | |         ||||||| |   |||||||| |||||||| |||||||| || ||||| ||||| || |||   || ||||||||||||||||| ||  ||||||  |||
taaccaattcattgtact---aattacttagtaatttccttatgttattatgttcactaatatgtcattatgtttacgatcacttccttttttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATTGGCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G01750.1 (Glycine max), 3'ss of exon 1
ggcttttatgttatatcttgcggtggttggtgttgggggagggtttatgtatagagaaattcgatattttttaa--atgtttgtgattgattttgtttt-------cagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG
     |||   |||   |||  ||  ||  |      | |   |   | |||    |  | |  || | | | |  ||||||  |||   ||    |||        |||||||| |||||||| |||||||| || ||||| ||||| || |||   || ||||||||||||||||| ||  |||| |  |||
-----ttaacctattcattgtagtaattacta----agtaacttccttatattagtatgtacactaatatgtcattatgtttacgatcacttcctctttgttgtaatagGTGTGGACACTGCAAAAAGCTTGCTCCAGAATATGAAAAGCTTGGTAGCAGCTTCAAGAAAGCCAAATCTGTTTTAATCGGCAAG

upper sequence: LOC_Os05g06430.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 1
ggcttttatgttatatcttgcggtggttggtgttgggggagggtt-tatgtatagagaaattcga-tattt---tttaaatgtttgtgattgattttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG
   |||    |||||| ||    ||   |   || | |     |  | |||   |   |||  || || ||   ||||     |||    || ||||  |   |||||||||||||||||||| ||||| || || || ||||| || || ||||| |||||||| || || || ||  | ||||| |||
---tttcgatttatatgttttactga--gaaattagagcttactgatgtgtgctgttgaatctgactaattgcatttatggaattggacatggttttaataatagGTGTGGTCACTGCAAGAAACTTGCTCCAGAGTATGAAAAGCTAGGGGCAAGCTTCAAGAAGGCTAAGTCTGTGTTGATTGCAAAG

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|163920132|gb|EG712050.1|EG712050
EST:     GAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
genomic: GAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|58662435|gb|CK051121.1|CK051121
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATATGAAAAACTCGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|58608597|gb|CK036630.1|CK036630
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCGTGGATATGAAAAACTCGGTGCAA
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCC-TGAATACGAAAAACTCGGTGCAA
EST: gi|58684543|gb|CK073230.1|CK073230
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATATGAAAAACTCGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|58653719|gb|CK042399.1|CK042399
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATATGAAAAACTCGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|88692194|gb|CI735769.1|CI735769
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|88732858|gb|CI756035.1|CI756035
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG
EST: gi|58654869|gb|CK043549.1|CK043549
EST:     AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATG                         GTGTGGTCACTGCAAGAAGCTTGCCCCTGAATATGAAAAACGGGGTGCAAG
genomic: AAGGAGGTCGGCCAGGACCGCGCCGCCCTCGTCGAGTTCTACGCGCCATGgtaataagcg ... ttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtatagagaaattcgatattttttaaatgtttgtgattgattttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG
                                     gattgat  putative branch site (score: 4)
                                           ttttgttttc  CT-rich tract
                  atattttttaaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttttatgttatatcttgcggtggttggtgttgggggagggtttatgtatagagaaattcgatattttttaaatgtttgtgattgattttgttttcagGTGTGGTCACTGCAAGAAGCTTGCCCCTGAATACGAAAAACTCGGTGCAAGTTTCAAGAAAGCCAAATCAGTCCTAATTGCGAAG

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