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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcattttcactctttatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt...

Basic information

species Oryza sativa
transcript LOC_Os03g52840.2
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 5
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaa-tcattttcactctt-tatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt
                        |  ||||||||||| ||||| ||||| |||||||||||||||||||| ||||| |||||||| |||||||||||||||||| || | |  | |||   | |      | | |||||   || |    |    ||||  || | |   ||| |  || |   ||     ||| ||||  
-----------------------GTTTATTGATATGGCAGAGTCCTTGTGTCAGAAACGTGCTTTGGAGGCTTTCCGTTTGGACCCGGCGAAATGGGGAGgtaaaatcttgtatagtctagcagcaatatctattatgttgccatgtcgtatgttccttttttgtgaac--atatctctttgcagtcaagcttttactgcac

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 5'ss of exon 5
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcattttcactctttatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctct---tttgtttcctgctt
                        ||||| || ||||| || || ||||||||||| ||||||||||| || || || ||||| || || ||||||||||||||||   | | |   | ||  |     |        | |  |||      |||    |||    | ||   | |||    |  |    | ||||   | ||
-----------------------GTACATGGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAGgtaaatacatatgatcatgtacgtcaagatagatgccatctgcatgtttcaaagca---atgtttttgaaattcttttctcaccatgaactggtttaaagttt

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 5'ss of exon 5
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcattttcactctttatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctct---tttgtttcctgctt
                        |||||||| ||||| || || ||||||||||| ||||||||||| || || || ||||| || || ||||||||||||||||   | | |   | ||| |     |        | || |||      |||    |||    | ||   | |||    |  |    | ||||   | ||
-----------------------GTACATTGACATGGCAGAATCCTTGTGCCAGAAGCGTGCTTTGGAAGCATTTCGGTTGGATCCTGCAAAATGGGGAGgtaaatacatatgatcatgtatgtcaagatagatgccatctacatgtttcaaagca---atgtttttgaaattcttttctcaccatgaactggtttaaagttt

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ32604 (Selaginella moellendorffii), 5'ss of exon 5
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcattttcactctttatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt
                        | |||||||||||||||||| |||||||||||||| ||  | || || || ||  |  | |||    ||||||||||||  |  || ||| |    |         |   ||  ||  | |    | |||                                              
-----------------------GTTCATTGATATGGCCGAGTCTTTGTGCCAGAAACGAGCACTAGAAGCTTTTCGTCTCAATCCAAACGAATGGGGAGgtacgtt-ttatcagtggcgaaaggataaagctctgacttcttttct-ttgcag----------------------------------------------

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|29674139|gb|CB670414.1|CB670414
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     CCAGAAACGTGC-TTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|25798315|gb|CA754276.1|CA754276
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     CAGAAACGTGCTTTGGAGGCCTTCCGCTTGTGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CAGAAACGTGCTTTGGAGGCCTTCCGCTTG-GACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     CAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
EST: gi|58691682|gb|CK080369.1|CK080369
EST:     CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAG                         TGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG
genomic: CCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcatt ... acctctgcagTGAATGTGCAACCTCTATCAGGGTCACCTGCCAACTTCCATGTTTACACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGGTTTTCCTTGCGTGCAGATACATTGATATGGCCGAGTCATTGTGCCAGAAACGTGCTTTGGAGGCCTTCCGCTTGGACCCAGCGAAATGGGGAGgtaaatcattttcactctttatcttgccttgtcatgtttttatatgaactccagctttcatgcgcatcaatagcctttagtcctcttttgtttcctgctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG