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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG

Basic information

species Oryza sativa
transcript LOC_Os03g21550.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G056462_T01 (Zea mays), 3'ss of exon 7
-----gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
     |   ||   |       ||||   |  |  ||    ||   || |   |||   |||| |     |  ||| | |  |||| |    |  | | ||| |||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| ||||| |||||||||||||| || ||||| |||
atgcggagaatcaacacaaatgtttttcaatttttta---atgtttttatttctaag--cttgctaaataattcttccttgtttttgtgcaatttcgctttttagATGAATATGTCATATGCAATGGTTGCAAGAGTCCGGATACCATTCTTTCTAAAGAGAACAGGTTGTTCTTCCTCCGATGCGAGCAG

upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 3'ss of exon 6
--gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactccttt-cagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
   ||||    ||   |        |  ||  | | |||     | |   | ||     |  |||  ||  |||  || |  ||  |  | | |   || |||| ||||| ||||| |||||||| |||||||| ||||||||||| ||||| ||||||||| || |||||||||||||||| ||||||
atttttacctcctaagtatgagatcgcagttttttttgtatacctttatctgaaaag--gaagtggaaaggttat-tcttacttgcacctgattgtgttgcagACGAGTACGTCATGTGCAATGGTTGCAAGAGCCCTGATACCATTCTTTCCAAGGAGAATCGGCTGTTCTTCCTTCGTTGTGAACAG

upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------gtttattctcttgttcctt-ttatga-ggtcctatgtgtgggattgtcattaaagtct---tgttgtgctaaac------------ttacatccttttttaatttcactccttt-cagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
                                                                               |      ||  |   ||   | ||   |   ||| ||| |||||| |  ||    ||       | ||||| |              |  ||| |   |  | |||| |   || ||||||||||||| || |||||||| ||||||||||| || || |||||||| ||||||||| || ||||||| |||||||| ||||||
gtaaggctcttcacttttgtattcttcatgtgtggtactaaaacaatatttgagcagttgcaagctgatatcgcttcgcgcacggacttctacaccccatcatattgagtctaagtgagggattatttttctgttccacacaatatgctagaaagggatgaaagactttatcttacatgtacttcattatgttgcagATGAGTATGTTATGTGCAATGGTTGCAAGAGTCCAGACACTATCCTTTCCAAGGAGAATCGGCTGTTCTTTCTTCGTTGTGAACAG

upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S93_178V6.1 (Physcomitrella patens), 3'ss of exon 6
gtttattctcttgttccttttatgaggtccta-tgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttt--taatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
 | ||   | |     |  |  || | |  |  ||  | |||    ||| |||     |||| | | | || ||||| ||||   | | |   ||  || ||||||||||||| || |||||||| || |||||||| || ||||||||| | ||||||||  | |||||||| |||||||| || |||
ctgtaccttttcagcgcaatattgtgcttttgctgcctcggaagtacatgaaa---cggttgggatgagctaacatcattttcactgactcatcttgttgcagATGAGTATGTTATGTGCAATGGTTGTAAGAGTCCGGACACCATCCTTACCAAGGAGAACCGTTTGTTCTTTCTTCGTTGTGAGCAG

upper sequence: LOC_Os03g21550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S386_20V6.1 (Physcomitrella patens), 3'ss of exon 6
---------gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
          || |   | ||||||  |  || | ||  | ||   |   | |     ||||| | |        ||  ||     | ||||   | | ||  || ||||||| || || || |||||||| ||||||||||| || || |||||| | ||||||||| |||||||||| |||||||| || |||
cctgcactccttcagcatgttgttc--tgcataatgttttctggaagaagtcg-----aaagtttcgcaaattctaa--taggatgtgttttggatcctcttgttgcagATGAATACGTTATGTGCAATGGTTGCAAGAGTCCGGACACTATCCTTACGAAGGAGAATCGGTTGTTCTTTCTTCGTTGTGAGCAG

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|88214500|gb|CI214349.1|CI214349
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|9865576|gb|AU101326.1|AU101326
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88205220|gb|CI205069.1|CI205069
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88273096|gb|CI388552.1|CI388552
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88490910|gb|CI428182.1|CI428182
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88416253|gb|CI535929.1|CI535929
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88219103|gb|CI220376.1|CI220376
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88850056|gb|CI091351.1|CI091351
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|58588566|gb|CF986874.1|CF986874
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTGGTATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|58597410|gb|CK007938.1|CK007938
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88530135|gb|CI457475.1|CI457475
EST:     AAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|89169705|gb|CI110064.1|CI110064
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|86415107|gb|CI069510.1|CI069510
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88263631|gb|CI367405.1|CI367405
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTTATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88273785|gb|CI394191.1|CI394191
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATAGATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGAGACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|86839841|gb|CI343749.1|CI343749
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|89174934|gb|CI111132.1|CI111132
EST:     AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA
EST: gi|88452062|gb|CI552770.1|CI552770
EST:     AGGAAGATTTGGTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCA                         ATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTNATACCATCCTTTCTA
genomic: AGGAAGATTTGCTCCTAAAAACTTTGAAGCCATACTTAGGAGATATATCAgtaagtttcc ... ctcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG
                             tccttttttaatttca  CT-rich tract
                            atccttttttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttattctcttgttccttttatgaggtcctatgtgtgggattgtcattaaagtcttgttgtgctaaacttacatccttttttaatttcactcctttcagATGAGTATGTCATATGCAATGGGTGCAAGAGTCCTGATACCATCCTTTCTAAGGAGAATAGGTTGTTCTTCCTTCGTTGCGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - -ctatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - cttgttg