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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaaatgttttccttggctttcccatttgctacagtttgtgactttatactcatatcacatattctgatttgtgctgtag

Basic information

species Oryza sativa
transcript LOC_Os03g63090.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G112015_T01 (Zea mays), 5'ss of exon 6
----------GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaaatgtttt--ccttggctttcccatttgct-acagtttgtgactttatactcatatcacatattctgatttgtgctgtag-------------------------------------
          || |||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| || || ||||||||||||||   | | |  |   | | ||| |  |  |  | |    | ||||    || |  ||     |   |   |  |||||    | |                                     
TATGTTTCAGGGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAGgtaagttcatacgcataagcataggcatggctttgagtttgtcgcttgttctcttttggtcgatagatgcaacgttgtttgtatgttggcagcgtactcacactattctgcttacatgaaccccag

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G118586_T01 (Zea mays), 5'ss of exon 7
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaaatgtttt--ccttggctttcccatttgct-acagtttgtgactttatactcatatcacatattctgatttgtgctgtag-------------------------------------
|| |||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||||||||||||||| || || ||||||||||||||   | | |  |   | | ||| |  |  |  | |    | ||||    || |  ||     |   |   |  |||||    | |                                     
GGCTATGATATCAGTTTCCTGATAACAAACTACCATTGTGAGGACATGCATAAGCACAAGCTCATAGATTTCATCGTGCAATTTATGGAGgtaagttcatacgcataagcataggcatggctttgagtttgtcgcttgttctcttttggtcgatagatgcaacgttgtttgtatgttggcagcgtactcacactattctgcttacatgaaccccag

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA08G11740.1 (Glycine max), 5'ss of exon 7
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaaatgttttccttggctttcccatttgc--tacagtttgtgactt-ta-----tactcatatcacatattctg-atttgtgctgtag------
|| ||||| || || ||||| |||||||| |||||||||||||| ||||| ||||| || ||||| || || ||||| || |||||||||| ||| ||   ||||  || |     |   ||||||  |  | |||||| ||| ||     ||   | || | | || ||| || | ||  ||        
GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTCATTGACTTTATTGTGCAATTTATGGAGgcaag-aattttgttgaccctataacttggatttgcattttattttgtggcttgtagtaattatctaaattagagatactgtatctatggagtgactatgg

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA05G28650.1 (Glycine max), 5'ss of exon 7
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaa------aaatgttttccttggctttcccatttgct--acagtttgtgactttatactcatatcacatattctgatttgtgctgtag--------
|| ||||| || || ||||| |||||||| |||||||||||||| ||||| ||||| || || || || || ||||| || |||||||||| ||| |        |   | || ||||| ||| |  |||  |   | | ||||     | ||   | || |   || ||| | ||  || | |        
GGATATGACATTAGCTTCCTTATAACAAATTACCACTGTGAGGAGATGCAGAAGCACAAACTTATTGACTTTATTGTGCAATTTATGGAGgcaagaattttgttgaccctattacttggatttgcattttattttgcggcttgtagtaat-tatctaaattaaggatactg-tatgatctatggagtttcta

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT4G14147.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaag--------gaaaaatgttttccttggctt----tcccatttgctacagtttgtgactttatactcat-atcacatattctgatttgtgctgtag--
|| ||||| || || || || ||||||||||||||||| || || ||||| || || ||||| || ||||||||| ||||||||||||||| |||        ||||  |  | |  ||    |     |    ||||| |  || ||  | |  ||   || |  | || |  || || |      |   
GGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGgcaagtctctctcgaaacctaatctttttattctatgaccttggttgctcccattagtagcatcctaacaatcaatatatgtcttggtt-gcatcaaacct

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: AT4G14147.2 (Arabidopsis thaliana), 5'ss of exon 8
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaag--------gaaaaatgttttccttggctt----tcccatttgctacagtttgtgactttatactcat-atcacatattctgatttgtgctgtag------
|| ||||| || || || || ||||||||||||||||| || || ||||| || || ||||| || ||||||||| ||||||||||||||| |||        ||||  |  | |  ||    |     |    ||||| |  || ||  | |  ||   || |  | || |  || || |      |       
GGCTATGACATAAGCTTTCTTATAACAAACTACCACTGCGAAGAGATGCAGAAACAGAAGCTAATTGATTTCATTATTCAGTTTATGGAGGCAAgtctctctcgaaacctaatctttttattctatgaccttggttgctcccattagtagcatcctaacaatcaatatatgtcttggtt-gcatcaaacctaatg

upper sequence: LOC_Os03g63090.2 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv05s0029g01310.t01 (Vitis vinifera), 5'ss of exon 7
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaagg-----aaaaatgttttccttggctttcccatttgctaca----gtttgtgactttatactcatat---cacatattctgatttgtgctgtag--
|||||||| || || || || ||||||||||| ||||||||||| ||||| || || ||||| || ||||| || || || |||||||||| |||      ||  |  ||||  ||  | ||  | ||| |||       ||| | |  |    ||  |||     | | || | |||||   | ||   
GGTTATGACATTAGCTTTCTTATAACAAACTATCACTGTGAGGATATGCAAAAACACAAGCTTATTGATTTTATCGTGCAATTTATGGAGgcaagttctctaatgaatttttttttaccattttcttttcctaacttatatttattaggtggctctggtatgtcttccttttgtaatttgatttctattt

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|218490476|gb|FG964035.1|FG964035
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGT
EST: gi|58657821|gb|CK046501.1|CK046501
EST:     GCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: GCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|218494510|gb|FG957958.1|FG957958
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|87033364|gb|CI187988.1|CI187988
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GGCATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|87036117|gb|CI189564.1|CI189564
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GGCATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|58652450|gb|CK041130.1|CK041130
EST:     GCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: GCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|218502090|gb|FG953891.1|FG953891
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|88969036|gb|CI099025.1|CI099025
EST:     TAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: TAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|33683667|gb|CF311906.1|CF311906
EST:     AAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|33683666|gb|CF311905.1|CF311905
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|86490261|gb|CI132894.1|CI132894
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
EST: gi|117226003|gb|CT845644.1|CT845644
EST:     AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAG                         GACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT
genomic: AGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaa ... tgtgctgtagGACATCGACAAGGAGATCAGTGAGCTAAAGCTTTCGGTAAATACACGTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTATGATATCAGTTTCCTGATAACAAACTACCACTGTGAGGACATGCACAAGCATAAGCTCATAGATTTCATTGTTCAGTTTATGGAGgtaaggaaaaatgttttccttggctttcccatttgctacagtttgtgactttatactcatatcacatattctgatttgtgctgtag

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