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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG

Basic information

species Oryza sativa
transcript LOC_Os09g37270.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G105253_T03 (Zea mays), 3'ss of exon 3
------tctgttt-----ttaatatcacttaacttattctcttcaaaaaa-aatcagt--------ttactgtcaa---cataa-tcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
       ||||         | || |     |||||||||   ||||| | |||   |        || || ||||   || || ||| ||||||||  || |||  |||    | |   |||||| ||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||| |||||||
gtaaagcctgtgcaaagacaagtaaccacctacttattctggccaaaacacaattgataaagtctttttctttcaattacacaaatcataatattcactttgtttctttgaaaatttc--ccagGATGTTGGGCAGTCCATACTTGAAAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATATATGTTGATGATG

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G158679_T01 (Zea mays), 3'ss of exon 4
-----------tctgtttttaatatcacttaacttattctct-------tcaaaaaaaatcag--tttactgtca---acataa-tcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
            |       |||| |  |  |||| ||||||       ||||||   ||||    || || |||   ||| ||  |||||| |||| |||| ||||||| || | ||    |||| || |||||||||||||| ||  | ||||||||||||||||||||||||||||||||||||||||| |||||||||||||| || ||||| |||||||
gtaaagctcatgcaaaaacaaataaccatggacttcttctctggccaaatcaaaatcgatcaagtctttctttcagttacacaaaccacaatcttca-ctttgtttcttgcgtgtttt---tagGATGTCGGGCAGTCCATACTTGAATGCTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCAAGAATTGATGATGTGATCTATGTTGATGATG

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G10330.1 (Glycine max), 3'ss of exon 4
-----tctgtttttaatat-cacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
     | |||  ||| | | || |||          |         |  || |  |||  || | ||    ||||  | ||| |     || | ||  |||  ||||| || || ||||| || || || ||||| ||||| ||  ||||||||||||| ||||||||||| ||||| |||||||||||  | |||||||| ||| 
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaagatggctgggaatagaa----aataagcttctgtggaatttcttttcgttg--cagGATGTCGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATTGATGATGTCCTATATGTAGACGATA

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G02620.1 (Glycine max), 3'ss of exon 4
-----tctgtttttaat-----atcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
     | |||  ||| |     || ||| |    ||| |  |    | ||    | ||      |||| ||    ||||  | ||| |     || | ||  |||  ||||| ||||| ||||| || || || ||||| ||||| ||  ||||||||||||| ||||||||||| ||||| || ||||||||  | |||||||||||| 
aatggtttgtgattagtgtacaattactaagaggattgtggttgggagaaggtggcttgg----aacagaa----aataagcttctgtggaatttcttttcattg--cagGATGTTGGACAGTCTATTCTTGAAAGTTATTCAAGAGTGATGGAGAGCTTGGCCTTTAACATAATGGCCAGGATAGATGATGTCCTATATGTAGATGATA

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G38430.1 (Arabidopsis thaliana), 3'ss of exon 4
tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
      |  | |||   ||    | | || | |       ||||      ||  |  ||  | | |  ||| |    ||| | | ||||| ||||  ||||| || ||||| || || || ||||||||||| |||||  |||||||| |||| || ||||| |  |||||||| ||||||||  ||||||| |||||||
-----gtacattatagtttggagtgtgctttgctggttgcatca------tgaaacgatgcttagataatttaagagtttgtgt-gtgtt-cttg--cagGATGTAGGGCAATCAATTCTGGAGAGTTACTCTAGGGTGATGGAGAGCATGGCCTTCAACATCACGGCCAGAATAGATGATGTGCTTTATGTTGATGATG

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv03s0038g03620.t01 (Vitis vinifera), 3'ss of exon 5
tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtc-cagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
  |  ||  | |       || | |  ||||| | || || |   |||    |  |   ||  |  |||  || ||  ||| ||| | |   ||||  ||||| || |||||||| || ||||| ||||| ||||||||  |||||||||| || || |||||||| || || || ||||||||  |||||||||||||||
gttagttccattggagaggaattaagcctcttgagaataagttgctttgacatagatgaaag-atgataaccagctcatttacttatctgcattgttacagGATGTAGGGCAGTCAATTCTAGAAAGTTATTCAAGGGTAATGGAGAGCTTAGCTTTCAACATAATGGCAAGGATAGATGATGTTCTTTATGTAGATGATG

upper sequence: LOC_Os09g37270.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ32418 (Selaginella moellendorffii), 3'ss of exon 5
tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtg-----tttcttg---tccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
                                                   || || ||  |   ||  ||| |     |||||   |     ||||||    || |||||||||| || ||||| || ||||| |||||  ||||  ||||||||||||||||||||||  | ||  | || || || ||  | |   | || || |
---------------------------------------------------gtaaagatctttcaaagcttcgttcgagtttctcacgagagctttctttcgttctagGACGTTGGTCACTCCATTCTGGAGAGCTACTCGCGGGTGTTGGAGAGCTTGGCATTTAACATCCTCGCTCGGATCGACGACGTCTTGTTCATCGACGACG

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|86496451|gb|CI139084.1|CI139084
EST:     AACAAGATCCAGTATAACAAG                         GACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
genomic: AACAAGATCCAGTATAACAAGgttattcctc ... tcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
EST: gi|33802569|gb|CF327157.1|CF327157
EST:     CTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAG                         GACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG
genomic: CTGGTTTGCCACAAACCTCTCTCGACATGAACAAGATCCAGTATAACAAGgttattcctc ... tcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG
                        ttcatctttttttctt  CT-rich tract
                    aatattcatctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtttttaatatcacttaacttattctcttcaaaaaaaatcagtttactgtcaacataatcacaatattcatctttttttcttgtgtttcttgtccagGACGTTGGGCAGTCCATACTAGAGAGTTACTCAAGGGTTCTGGAGAGCTTGGCATTTAACATAATTGCCAGAATTGATGATGTAATTTATGTAGATGATG

tctgttt
- - - - - - - - - - - - - - - - caaaaaa
- - - - - - - - - - - - - - - - - - - - - - -tttactg
- - - - - - - - - - - - - - - - - - - - - - - - - - -caacata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaata