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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacacatatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g07130.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 21
gtcacacatatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctt-taatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG
          ||||  |   ||   | ||  | | || ||     ||     | || | |  | |||||    |  |  |  ||||||||||||| || ||||||||||| |||||||||||||| ||||| ||||| || |||||||||||||| ||||||||||||||  | | | |          |
---------gtgatgatacatttgactttcctcttcttga---tcaaatgcgatat-gtctgagctaatgatgtgattgttctcatgtagATGCCACTACACACCATAATCGAGATACAAATGGGCGTCACGGGTGTGGAAGAGAAGAGGTACAAACTCATGGACTGAATGAATACATAAAAGCAGCTGG

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 22
gtcacacatatgatcttctcttgttcattattgtgctagaaacctaaga-aatacatag---accaaactaataccctttaatcttcatg----------tagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG-
 | || || || || || |    |  |||  | | |||| |    || | ||| || ||    ||||  ||   ||    || ||| |||           || | || || || || ||||| ||||||||||||||||| || |||||  | ||||| || |||||||||||||||||| |   | | ||   |  ||    
-ttac-cacatcattttatga-ataaattccttttctaggagaagaaaacaatccaaagttggccaagttacaccctgacaaacttaatgattcacttttcagGTACCGCTTCATACTATAATAGAGATACAAATGGGAGTTACTGGTGTCCAAGAGAAAAGATACAAGCTCATGGACTGACTTCGC-TTCACAGAATCTTTTG

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 22
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 23
----------gtcacacatatgatcttctcttgtt-cattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG
            ||   || || | | | ||  || || |  | |     |   ||  | || |   | |   | || || |    |        |  ||||||| || |||||||| |||||||| ||||||||||| || ||| || |||||||  | || |||||||||||    |   | |               
tccagctattagcagctatctggtttgcactgattgcacttctattgccaacttctctggaacatgaacatatagctcattcaagatttggagtgttcagATGCCACTTCACACCATTATTGAGATTCAAATGGGAGTAACCGGTATTCAGGAGAAACGATATAAGCTCATGGA---GACCCAAA---------------

upper sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 22
lower sequence: PP1S242_66V6.1 (Physcomitrella patens), 3'ss of exon 23
----------gtcacac-atatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG
           ||  |   | |   ||  |   | || |  |   ||      | |    || | | | | | |||| || | |  |    ||     ||||||| || || || || |||||||| ||||||||||| || |||||| |||||||| | ||||||||||||||    |   | |               
tttccttgatatcgaattgtttctgctatttgcggtcttgttcacgccgtttgcattttcaacatacataactaactcattcacaattcgatttgcacagATGCCACTGCATACTATTATTGAGATTCAAATGGGAGTTACTGGTGTTCAGGAGAAGCGATACAAGCTCATGGA---GACCCAGA---------------

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|58611022|gb|CK038734.1|CK038734
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86850852|gb|CI338828.1|CI338828
EST:     TATATGCATATTTCGCTTACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29629510|gb|CB634519.1|CB634519
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACCCCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29616012|gb|CB621024.1|CB621024
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|16578926|gb|BI813021.1|BI813021
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACCAAATGGGAGTCACAGGTGTTGA
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATAC-AAATGGGAGTCACAGGTGTTGA
EST: gi|86842389|gb|CI335281.1|CI335281
EST:     ATATGCATATTTCGCTGACAGGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTTTTGAG
genomic: ATATGCATATTTCGCTGACA-GGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86838836|gb|CI330278.1|CI330278
EST:     TATATGCATATTTCCCTGACAGGCCTCTGA-GGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29612782|gb|CB617795.1|CB617795
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29615977|gb|CB620989.1|CB620989
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86868850|gb|CI334222.1|CI334222
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86853669|gb|CI330520.1|CI330520
EST:     TATATGCATATTTCGCTGACAGCCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|88844562|gb|CI020409.1|CI020409
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29615975|gb|CB620987.1|CB620987
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|29616052|gb|CB621064.1|CB621064
EST:     TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
EST: gi|86869030|gb|CI335597.1|CI335597
EST:     TATATCCATATTTCGCTCACAGGCCTCTGAGGGAAGTCCCAGATATTGAG                         ATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG
genomic: TATATGCATATTTCGCTGACAGGCCTCTGAGGGAAGTCCCAGATATTGAGgtcacacata ... cttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG
                                            tcttcat  CT-rich tract
          taagaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacacatatgatcttctcttgttcattattgtgctagaaacctaagaaatacatagaccaaactaataccctttaatcttcatgtagATGCCTCTCCACACCATAATTGAGATACAAATGGGAGTCACAGGTGTTGAGGAGAAGAGGTACAAGCTCATGGACTGAATATACATACATCTAGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA