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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcttggggagtttcaatctgtagtgagcctgtaaatttgtagctggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG

Basic information

species Oryza sativa
transcript LOC_Os03g16110.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 2
---cttcttggggagtttcaatctgtagtgagcctgtaaatttgtagctggtggctctaaggtgt-gtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
   ||  ||     | |  || || | |     |||| | | |||  |   || ||  |  |  | |||| ||| |    | ||   ||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| ||||| || ||||| || ||||||||||||||||||||||||||||||||||||||
tttctatttttactgatgaaagctttgga----ctgtgattgtgtgtcctttgtcttcattgaatagtatctaagtgcaatctccactgtcatttggtatccagGTGACATCCATGGTCAATACAGTGATCTTCTAAGGCTTTTTGAATATGGAGGCTTTCCTCCTGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG

upper sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G41890.1 (Glycine max), 3'ss of exon 1
---cttcttggggagtttcaatctgtagtgagcctgtaaatttgtagctggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
     | ||   |   || |||   | || ||| | |  ||||        ||||| ||  ||   | | |  | |  ||   |  | || ||   | | |||||||||| ||||| |||||||||||  |  ||||||| ||||||||||| ||||| || ||    || |||||||| || || || || || || || ||
tattgttttaatgttgttgaattgtttgttagcttttctattt---aacattggctgtagtgttattttatggcatggttgagatctctctttgctttttcagGTGACATTCATGGGCAGTACAGTGATTTGTTAAGGCTATTTGAGTATGGGGGTTTGCCTCCTACTGCGAATTATCTCTTTTTGGGGGACTACGTGGACCG

upper sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G29400.1 (Arabidopsis thaliana), 3'ss of exon 1
cttcttggggagtttcaatctgtagtgagcctgtaaat--ttgtagctggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
  |  |      ||||   |   |||    |  | | |  | ||| ||| |    |     |   ||  |    |  || |   ||||| |||  | |  |||||| || ||||| |||||    || ||  | ||||||||||||||||| || || || || ||||| |||||| | ||||| |||||||||||||| ||
--tgataaaacatttcctgcaaaagtttaacgttgactagtagtatctgatatgccatgttttcttagatgtaatggttatattttgtcttttactttatagGTGATATTCATGGGCAGTATTCAGATCTATTGAGGCTTTTTGAGTATGGAGGGTTCCCTCCCGAAGCTAATTATTTGTTCTTGGGTGATTATGTTGACCG

upper sequence: LOC_Os03g16110.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv06s0004g05530.t01 (Vitis vinifera), 3'ss of exon 1
cttcttggggagtttcaatctgtagtgagcctgtaaatttgtagctggtggctc------taaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
     | ||  || | ||| ||         |  || |||||| |   ||| |       |||  | | |||||    || |  |    | |   ||| | ||||||||| || ||||| || |||||||| ||| ||||||| ||||| ||||| || | ||| || |||||||||||| ||||  |||| || ||||| || ||
-----ttggttgtgttaat-tgcctcagaagttaaagtttgtaaccattggtttgtctgttaatttatttatttgttgttctcctttgatttttgttgatctccagGTGATATTCATGGGCAATACAGTGATCTTTTAAGGCTCTTTGACTATGGGGGATATCCTCCTGAAGCCAATTATTTATTTCTAGGGGACTATGTGGACCG

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|29680082|gb|CB676357.1|CB676357
EST:     CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCG                         GTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
genomic: CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCGgtacgtgctc ... tggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
EST: gi|300216266|gb|HO088051.1|HO088051
EST:     ATCAAGATCTGCG                         GTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
genomic: ATCAAGATCTGCGgtacgtgctc ... tggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
EST: gi|86895159|gb|CI310329.1|CI310329
EST:     CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCG                         GTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
genomic: CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCGgtacgtgctc ... tggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
EST: gi|86884055|gb|CI311575.1|CI311575
EST:     CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCG                         GTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
genomic: CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCGgtacgtgctc ... tggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
EST: gi|33681576|gb|CF309815.1|CF309815
EST:     CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCG                         GTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG
genomic: CCTCAGCCAGCCCAATCTCCTCGAGCTCGAGGCGCCCATCAAGATCTGCGgtacgtgctc ... tggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG
                   atttaac  putative branch site (score: 3)
                         cttttttttcacttgt  CT-rich tract
                  tatttaactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcttggggagtttcaatctgtagtgagcctgtaaatttgtagctggtggctctaaggtgtgtatttaacttttttttcacttgtcatttggtatccagGTGACATCCATGGTCAGTACAGTGACCTTCTAAGGCTTTTTGAGTATGGTGGTTTTCCCCCAGAAGCCAATTATCTATTCTTAGGTGATTATGTTGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
cttcttg
- - - - - - - - - - - - - gagcctg
- - - - - - - - - - - - - - - - - - - - - -gctggtg