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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT

Basic information

species Oryza sativa
transcript LOC_Os12g30020.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 4
gtatgctattgatacccttattatctttagagatatcact---caatcatgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
|||||||| || |||||||| | || || || ||  || |   || |  ||||| ||  ||  | || |    ||  | ||||||| ||||||||||||||||||||||| ||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
gtatgctagtgctacccttactgtcgtttgaaattgcagttcacagttgtgtatctactacacttaata--ttgtgcactgtacagACTGCGTACTTCGCTTTGCCTGCAATTCGAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G377311_T01 (Zea mays), 3'ss of exon 5
gtatgctattgatacccttattatctttagagatatcact---caatcatgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
|||||||| || |||||||  | ||||| || ||  || |   || |  ||||| ||  ||  | ||   |  ||  | ||||||||||||||||||||||||||||||||||  ||||||||||||||||||| |||||||||| ||||||||||||||||||||||||||| || |||||||||
gtatgctagtgctaccctttctgtcttttgaaattacagttcacagttgtgtatctactacacttaat--gttgtgcactgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTTGAGCCTCATCATATTGCAGCTGGTGCTATCTATTTGGCTGCTAAATTTCTCAAAGTGAATCTCCCATCTGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
gtatgctattgataccctta--------ttatctttagagatatcactcaatcatgtatataacacgttaaaaag-ggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
||||| | | | | || ||         ||| ||| |  ||  | | |   |  |  |||||     | | | |  ||    |    | ||||||| | || ||||| |||||||| || ||||| ||||||||||| |||||||| || ||  | ||||| || ||  | ||||||||||||||||| |||
gtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttt-taaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G02880.1 (Glycine max), 3'ss of exon 4
-----gtatgctattgataccctta---ttatctttagagatatcactcaatcatgtat-ataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
      | || |    ||    ||    ||| || | ||  |||   | ||  || | | || ||||  |  |||       |    | ||||||| | || ||||| |||||||| || ||||| ||||||||||| |||||||| || ||  | ||||| || ||  | ||||||||||||||||| |||
gtatgatttggttgcaatttgtttgaatttaactgtcgatttatttttaaaatatatttgatcacacactggaaaaaa---gtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G02860.1 (Glycine max), 3'ss of exon 5
---------gtatgctattgatacccttattatctt-tagagatatcactcaatcatgtat-ataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
         |  ||| |||  |     | | |   | | ||  |||   | ||  || | | || ||||  |  |||       |    | ||||||| | || ||||| |||||||| || ||||| ||||||||||| |||||||| || ||  | ||||| || ||  | ||||||||||||||||| |||
gtatgatttggttgcaatttgtttgaatttaactgtgtcgatttatttttaaaatatatttgatcacacactggaaaaaa---gtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtatgctattgatacccttattatctttagagatatcactcaatca---tgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
                       || |    ||  |     |   || |  |  | | || ||   ||    | | |    |||    | |  ||         | ||||||| | || || || |||||||| || |||||  | || |||||||||||||| || ||  | ||||| || ||||||||||||||||||||||| |||
gtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactggaaagcggcttgcagGCTGAGGACATCACTCTGCCTGCAATTTAAGCCCGACCACATTGCAGCAGGTGCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaaagggcgta---tattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
                || ||| | ||| ||   |||| |  |   |  ||   | |     | ||   ||   | | |   | | |||   |||||| ||| || || || || ||||| || || || ||||||||||||||||| || || ||||||||  |||||||||| ||||| || |||||  | ||    || 
caaaaaacttttcagagtttgccagtga-acgaatatt-ttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S264_33V6.3 (Physcomitrella patens), 3'ss of exon 5
------gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaa------------agggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
       | ||| |  |  | |  |||||       | || |      | ||||| | |  || || | ||             |||      |||| ||| || || || ||| | |||||||| |||||||||||||||||||| || || |||||||| |||||||| || ||| | |||||||| || ||    |||
ttagagatttgccag-gtaagctatattacagaagaacatgtttaatgagcatgtctgttgcaagtgagaatagctgaggcaaggggaaagggttgtgcagTCTTCGCACATCGTTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTTTTGAAAGTGAATCTGCCCAAAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 3'ss of exon 4
---------gtatgctattgatacccttattatctttagagatatcactcaat---catgtatataacacgttaaaa--------agggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
          | ||| |  | ||  | |||| |    |   | ||     |||   ||||| | |  || || ||          | || |    |||| ||| || || || ||||| || ||||| || || |||||||||||||| || || |||||||| |||||||| || || || |||||||| || ||    |||
tccatagagatttgcca--ggtaagcctatttttcagaagaacat-gtgtaatgtacatgtctgttgcaagtgaatggctgaggcaaggggagggttgtgcagCCTTCGCACCTCGCTATGTCTGCAATTTAAACCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTCCTTAAAGTGAACCTCCCCAAAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S80_193V6.1 (Physcomitrella patens), 3'ss of exon 4
------gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaa------------agggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
       | ||| |  |  | |  | |||         || |      | ||||| | |  || || | ||             |||      |||| ||| || || || || || |||||||| |||||||||||||||||||| || || |||||||| |||||||| |||||||| |||||||| || ||    |||
ttagagatttgccag-gtaagctatgttacagaagagcatgtttaatgagcatgtctgttgcaagtgagaatggctgaggctaggggaaagggttgtgcagTCTTCGCACATCACTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAATTTCTGAAAGTGAACCTACCCAAAGAT

upper sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S86_187V6.1 (Physcomitrella patens), 3'ss of exon 5
------------gtatgctattgatacccttattatctttagagatatcact-caatca-tgta-tataacacgttaaa--aagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
             |  |  ||    |   | ||  |||||      |  |||   | || |||| |   | | | |||   ||||| |  |||||| ||| || || || || ||||||||||| || |||||||| || || || || || ||||||||  | |||||||| |||||||||||||| || ||    || 
caagatgccacttttagagatcagcagattaatgttctttgtgctgaaaactgtgaccactgtagtcggaaaggctaatgtaagggtgattattgtccagACTTCGCACGTCACTTTGCCTGCAATTTAAGCCTCACCACATCGCTGCGGGAGCTATCTTCCTCGCTGCTAAGTTTCTCAAAGTGAATCTGCCGAAGGAG

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|3106565|gb|D42282.1|D42282
EST:     GTTGCTCAAAATGCGCTTGCTCAGGTTGCATGGAATTTTGTCAATGATGG                         GCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGG
genomic: GTTGCTCAAAATGCGCTTGCTCAGGTTGCATGGAATTTTGTCAATGATGGgtatgctatt ... tattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGG
EST: gi|58656723|gb|CK045403.1|CK045403
EST:     GTTGCTCAAAATGCGCTTGCTCAGGTTGCATGGAATTTTGTCAATGATGG                         GCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCA
genomic: GTTGCTCAAAATGCGCTTGCTCAGGTTGCATGGAATTTTGTCAATGATGGgtatgctatt ... tattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCA
EST: gi|29677818|gb|CB674093.1|CB674093
EST:     GTTGCTCAAAATGCGCTTGCTCAGG--GCGT--A-TATTGT-AC--A-GG                         -CTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGG
genomic: GTTGCTCAAAATGCGCTTGCTCAGGTTGCATGGAATTTTGTCAATGATGGgtatgctatt ... tattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagatatcactcaatcatgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
                     atataac  putative branch site (score: 3)
             aatcatgtatataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctattgatacccttattatctttagagatatcactcaatcatgtatataacacgttaaaaagggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC