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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtactactatttcttttgcatgttcagtctccagtactatccattaaaagtttattcttttgttgatcagatgctaatcatgctaaccctcataaatgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT

Basic information

species Oryza sativa
transcript LOC_Os11g08300.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G060800_T02 (Zea mays), 3'ss of exon 1
--gtagtact-actattt-cttttgcatgttcagtctccagtact-atccattaaaagtttattcttttgttgatcagatgctaatc--atgctaaccctcataaatg-atgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT
   |  || | | |||   | | ||||  |  ||  ||||| |   ||  |||      |  | ||  ||    |      ||   |   |||||||| |     ||   || |||||||||||| ||| | ||||||||||| ||  | || ||||| ||| | ||||| || || ||||| ||  |||||||||| ||||||||||||||| 
gtattttatttattatccacctctgcaactggagcttccaggagagataaatttgtttctcctcctgctgccactgtttatctggcccggtgctaaccttttgggattcgtgctcagGTACCTGCGGCCATAACTACATTCCCGTCCTCCGCCCAAATCGTGCCGGAGCCCCTCGGCGTCGTGCTCATCATCTCAGCCTGGAACTACCCTTTCA

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G44170.3 (Arabidopsis thaliana), 3'ss of exon 2
gtagtactactatttcttttgcatgttca-gtctccagtactatccattaaaagtttattcttt-tgttgatcagatgctaatcatgctaaccctcataaatgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT
                        |||   |  |  ||||   |   ||     || ||  | | ||||  | || ||||||||||  |     |  |   |     ||||| |    |  | || || || || ||  || | ||  | |||||||| |||||||||||||| || ||||| ||||| || |||||||| |||||  
------------------------gtttgtgctttgagtagagtttgtt-----ttcatcatatatgttattaagttgctaatcattgttctgtttttcggt-----tcagGCAAAGACTTCTCTAACAACGTTTCCTGCATCCGCGGAGATTGTGTCTGAGCCTCTTGGTGTTGTGCTAGTGATCTCGGCTTGGAACTATCCTTTTC

upper sequence: LOC_Os11g08300.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv07s0031g02630.t01 (Vitis vinifera), 3'ss of exon 4
---------gtagtactactatttcttttg----------catgttcagtctccagtactatccattaaaagtttattcttttgttgatcagatgctaatcatgctaaccctcataaatgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT
         ||   || |||||||                || ||   ||        ||  || |  ||| | || | || |||   | || |   | | |||| |||   |    ||  |   ||||      |  |  | || ||||  |||||| | ||| ||||||||||||| ||||||||||||||  | ||||||||| ||||||| || ||||| |
gtaattagtgtcaaaccactattttagccaggaataataacaagtagtgtggtttcagctgcccttgtaaactgtaattttatgtc--ttag-tataatttatgcaaacttcctcgcatttt---cagGCCAAAACTTCAATGACAACATATCCATCATCAGCAGAAATTGTGTCAGAACCTCTTGGTGTCGTGTTGGTCATCTCAACATGGAATTATCCTTTGT

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|29680879|gb|CB677154.1|CB677154
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|29660175|gb|CB656450.1|CB656450
EST:     CTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACACTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGA
genomic: CTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAAC-CTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGA
EST: gi|88433183|gb|CI569852.1|CI569852
EST:     GCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCC-ATCAAATGCGCAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58695219|gb|CK083906.1|CK083906
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58604207|gb|CK014735.1|CK014735
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|29645892|gb|CB650899.1|CB650899
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|29643971|gb|CB648978.1|CB648978
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58689115|gb|CK077802.1|CK077802
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58691525|gb|CK080212.1|CK080212
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58695788|gb|CK084475.1|CK084475
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|58690002|gb|CK078689.1|CK078689
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|33675935|gb|CF304174.1|CF304174
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|29630144|gb|CB635153.1|CB635153
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACGACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|29681705|gb|CB677980.1|CB677980
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG
EST: gi|33800254|gb|CF325992.1|CF325992
EST:     CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAG                         GTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAATTTGTGTCAGAG
genomic: CCTGCACATTTGCCTTGAAGGGGTTGAAGAATTGGATGAAACCTGAGAAGgtagtactac ... tgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcttttgttgatcagatgctaatcatgctaaccctcataaatgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT
                             tgctaac  putative branch site (score: 1)
                                        ataaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtactactatttcttttgcatgttcagtctccagtactatccattaaaagtttattcttttgttgatcagatgctaatcatgctaaccctcataaatgatgatcagGTACCTGCCGCCCTCACTACATTCCCATCAACTGCACAAATTGTGTCAGAGCCTCTTGGTGTCGTCCTAGTCATCTCAGCATGGAACTACCCTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA