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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA

Basic information

species Oryza sativa
transcript LOC_Os05g40820.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G110328_T03 (Zea mays), 3'ss of exon 4
atgctcaattccttgtatatatgtacagttagtcatgctatg--tattgcttc-cgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
       | |   | | |  |   ||| ||| ||  || |    ||||    | | |  ||   |   |  ||||||    ||  | |||| |||| | | |||||||||||||||| ||||||||||||||||||||| ||||||||||||||||||| ||||| ||||| ||||||||  | || || ||||| |||||||
-catctgaataaatctttgcaacaacaattactctcgccacacttattatggcgctaaaagtctagaaccttttacatgtattagccattt-ctgtctgt-agGATATCCATGCTGAGGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCCTAGAGGTGATCCAGAAGAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G074898_T03 (Zea mays), 3'ss of exon 4
atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttccca-attttctgttttt---tagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
     ||| |    |  |  |   ||| ||  |  ||| |||       |      |||    |   |  |     |||      ||||    ||| |   ||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||||| ||||| ||||| |||||||| |||||||| ||||| |||||||
----ccaactagacgattgcaacaacaattgtttctgccatgctaacaatggtgctagaagtctagagcctctgatcttaaatgtatttgtcatttgtctgtagGACATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCGAGGTCCATTGTGGGTGCTTCCTTGGAAGTGATCCAGAAGAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G142640_T02 (Zea mays), 3'ss of exon 5
------atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
          |  ||    |     | || | | ||| |  ||| |||  |    |      | |    |   | |||||  ||||     |||| |  | | |||||||||||||||||||| || ||||||||||||||| ||||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||
atcgatccatttgatcatgtcatcgtttgca-aattatttctgccatgcttataatagtgctataagtctatagcttacatgcttt-----tttttttgtctgtagGATATCCATGCTGAAGCGGTAAAGAAGAGGCGCCGCGCCACCAAGAAGCCATACTCCAGGTCAATTGTGGGTGCTTCCTTGGAAGTAATCCAGAAGAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 3
atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttc-tgt--tttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
    |   ||  |||| |  ||||   ||     |   |   || |  | | |    | |    |   |||  |    ||     | | | |||  | | ||||| ||   |   |||||||| ||||||||| | ||| |  |||| ||||| ||||||||||| |||||||||||  |  ||||||| ||||| || ||||
---attggttgtttgtgtgcatgtcatgtgtaggacattgcttagtaatactgcaatggttgcatgcatttgaattgattgtttgtgtgcatgtcatgtgtagGACATTGCTCAAGAAGCTGTGAAGAAGAGGAGACGCGCTGCCAAAAAGCCTTACTCTAGGTCCATTGTTGGTGCCACTCTGGAAGTTATCCAGAAAAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G53020.1 (Arabidopsis thaliana), 3'ss of exon 3
---------atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
         |  |||| |   ||| || | | |   |||  |  | || ||| ||  |||  ||         | |||| |||  ||    |   | | | |||| ||||||         || ||||| ||||  ||| | ||  ||||||||||||||||||| ||||| |||||||||||| | |||||||| || || |||||||
gtaaaaaaaaaactcagtaatttggatctgtttt--gttgtttgtactttgttttttttc--attgatcctgatttgttaacattctaaaact-ctgtttcttttatagGATGCAGCACAAGAGGCTGTGAAGAGAAGGAGACGTGCCACCAAGAAGCCATACTCAAGGTCCATTGTTGGTGCTACCTTGGAAGTAATTCAGAAGAAGA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0100g00650.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
                                               |  |||    ||  |  || |   | | |  | |  | | ||| ||  ||   |   ||||| | | |  |  ||| |      |||   ||| |||| ||    || |||||||| ||||||| |||||||||| | |||||||||||||| ||||| || || |||||  | ||||| || || || ||||  |
gtaatcaaattttaaaattgtttggctatcaactcattttttgcctttttattgtgggtgaaagtgcattttcacttctaccctat-ttgtttgggaagtggctaattcagctgattcttttttctg---ctctcactttcagGACATTGCAGCAGAAGCTGTTAAGAAGAAGCGCCGCACCGCAAAGAAGCCATACTCAAGGTCCATAGTGGGTGCCACATTGGAGGTTATACAGAAGAGAA

upper sequence: LOC_Os05g40820.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv08s0007g04210.t01 (Vitis vinifera), 3'ss of exon 3
---atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
   ||      ||   |   | | || | |   |      ||||| |||   |  | |  ||   |||   |||    |  |       ||  ||    | |||||||   |   || ||||| ||||||||||| ||  ||||||| ||||| ||||||||||| ||||| |||||| | ||||| || ||||| ||||  |
tgtatatgtgttttggtcactttctggaaaagaatatccactatggattatgtttgttgggagttatttgttttgagtcactaattgggttaatgc---tcagGATATTGCTCAAGAGGCTGTAAAGAAGAGGCGTCGTGCCACCAAAAAGCCCTACTCTAGGTCCATTGTGGGTGCTACATTGGAGGTTATCCAGAAGAGAA

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|88397656|gb|CI684589.1|CI684589
EST:     AGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGAAG                         GATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCA
genomic: AGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGAAGgtattgtatc ... tgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCA
EST: gi|86417460|gb|CI031669.1|CI031669
EST:     AGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGAAG                         GATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCA
genomic: AGCCTGCAAAGCTTACCTGGACAGCCATGTACAGGAAGCAGCACAAGAAGgtattgtatc ... tgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA
                             ccctttcccaattttc  CT-rich tract
                                      aattttctgtttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgctcaattccttgtatatatgtacagttagtcatgctatgtattgcttccgatcagataaattctgtttacaccctttcccaattttctgttttttagGATATCCATGCTGAAGCTGTCAAGAAGAGGCGCCGCACCACCAAGAAGCCATACTCTAGGTCAATTGTTGGTGCTTCGTTGGAAGTCATCCAAAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG