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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g03820.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AC183590.4_FGT001 (Zea mays), 3'ss of exon 2
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcc-tataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                    | || | || ||| | |||||  |    ||| ||    |  | | |     |||   |    |  |||   | |||  | |||||    | ||  ||   || |||||||| |||||||| |||||||||||||||||||||||| |  ||||||| ||||||||||||||||||||||| ||||| |||
--------------------tatata-ctatag-tattctaataccatagttttagaaaactttgttggcaaacacgcccttactgttttgtgtaacatctaatg----aaataattggcttgtagGGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTTGTACTCTTGGCCTTGATATGATGTTCCGAACATGTACTGTGCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G459896_T01 (Zea mays), 3'ss of exon 3
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                                                                      |||        |  | ||  | |||  | |||||    | ||  ||   || |||||||| |||||||| ||||||||||||||||||||||||||  ||||||  ||||||||||||||||||||||| ||||| |||
---------------------------------------------------------------------gtaatgactattactgttttgtgtaacatctaatg----aaataattggcttgtagGGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTGGTACTCTTGACCTTGATATGATGTTCCGAACATGTACTGTACAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 4
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                      | |    | |    | || |  |||   |||| |  | ||   | |   ||     |  |  | ||| | |||  | |||||      ||  ||  ||| |||||||| |||||||| ||||||||||||||||||||||||||  ||||||| ||||||||||||||||| ||||| ||||| |||
---------------------atgactgatgactcatactgtagatt---tgtt-cagatatgccttaggcaatgactgttactgtttcatgtaacatctaatgaaaacaataattggtttgtagGGAAGATACGAAATAATGAGGAATTACATGCCTAAAGTTGGTACTCTTGGCCTTGATATGATGTTCCGGACATGTACTGTGCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AC203352.3_FGT001 (Zea mays), 3'ss of exon 1
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGA------ATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                     | |||        ||    || | |  ||  |||   | ||||     | ||        |  | ||  | |||  | |||||    | ||  ||   || |||||||| |||||||| ||||| |       ||||||||||||||||||  | ||||| |||||||||||||||   ||||| ||||| |||
-------------------gagaaaaatgaccaattactcat-actgtagctttgttcagatatgcggat-aatgactattactgttttgtgtaacatctaatg----aaatcattggcttgtagGGAAGATACGAAATAATGAGCATGTACAGTTACATGCCTAAAGTTGGTACACTTGGCCTTGATATGATGTTCTACACATGTACTGTGCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G020096_T01 (Zea mays), 3'ss of exon 4
gtagttttggccttagaccttgtaaa--gctttagcttttctatga-attcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                  ||  |||    || |||| ||  |  || || |  |   || ||   |   |  || |||          ||| |   |||   | |||      ||  |    || |||||||| ||| |||| ||||||||||||||||||||||||||  | ||||| ||||||||||||||||| ||||| ||||| |||
------------------ctgataactcactgtagccttgttcagatatgccttagggcttaggcaacgatttttact----------gtttcgtgaaaacctgatgaaaacaatcatcggcttgtagGGAAGATACAAAATAATGAGGAATTACATGCCTAAAGTTGGTACCCTTGGCCTTGATATGATGTTCCGGACATGTACTGTGCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA08G01750.1 (Glycine max), 3'ss of exon 5
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                   |    | |   ||   ||| ||  || | |    ||   |||  | |  ||| || |   ||  | |    ||     |||    ||     ||||| |   | ||||||| ||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||| | ||||||||||| |||
------------------gtcagcaggtcctattctttgtagtaactgaactatg---acagttctttcttgaccttt-agtggtgcaattacctgctttctgactatgtgttgttgc---acagGGAAGATACGACATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTACAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA05G37850.3 (Glycine max), 3'ss of exon 5
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                        | ||  ||   ||| ||  |||| |    ||   |||  | |  ||| || |   ||  | |    ||     |||    ||  |  | |||  |  | ||||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| ||||||||| | ||||||||||| |||
--------------------cagcaggccctattctttgtagtaattgaacaatg---acagttctttcttgaccttt-agtggtgcaattacctgctttctgactatatgt-gttgttgcacagGGAAGATACGACATCATGAGGAACTACATGCCTAAAGTTGGCTCTCTTGGGCTTGACATGATGTTCAGGACATGCACTGTGCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT4G23100.3 (Arabidopsis thaliana), 3'ss of exon 5
----------------------------------------------gtagttttggccttagaccttgtaaa--gctttagcttttctatgaattcagtgttgcctacatatttaacttaa-----cttacgagaagggttcctataaattttaatgcttcagattgt-ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                                               | ||||     | |||   | | |   | ||   | |  | |    |    |  |  ||   | |||   ||||     | || ||  ||     |  |||  ||| |        | ||| |||| |  |||| || ||||| |||||||| || |||||||| ||||||||  | ||||| |||||||||||| ||||||| || |||||||||
gtatgacgctttctctattcttaagattgaagaaagttaacatctgtttgtttctaattcagataatattatctgattctacatagccaacgttcggattatttcttggtgtttgtgttaagttttcctatgacgagtcaggcagtaagatttgacatagtgtaatgtgttctgtgcagGGGAGATACGACATTATGAGAAACTACATGCCGAAAGTTGGTACCCTTGGTCTTGATATGATGCTCCGAACGTGTACTGTTCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 5
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttat-agGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
         |   | ||| || | |   | | ||||||| ||   |  |  |||     |   || | | |    |||    |    |   |||    || |     || | ||||| |   | ||||||| ||||| |||||||||||||||||||| ||||||||||| ||||| ||||||||||||||  ||||||| |||||||||
---------gtacttgactttttgatcatgttgcttttccat---tctatggtt-----cgatttcagccttttgtactttgattacttgcata----ttga-----catagtgtttttggctcagGGAAGATACGAGATTATGAGGAATTACATGCCCAAAGTTGGCTCACTTGGACTTGATATGATGTTTAGAACATGTACTGTTCAG

upper sequence: LOC_Os05g03820.2 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 3'ss of exon 4
gtagttttggccttagaccttgtaaagctttagcttttctatgaattcagtgttgcctacatatttaacttaacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                |  ||  || | ||  | |  | | ||     |  | ||     ||| | | | |   |  |     |        | ||  ||    || || ||||||     | |||| ||||| || || ||||||||||||||||| |||||||| ||  | || || || ||||||||||| |||||||| ||||||
----------------atatttcaatggtt--ggtggtttgtgccagaaaggctggagggataat-atcctgggtgcctttcggatcgttagtgaacatt----ctgca-attgttggaa-acagGGCAGGTATGAGATAATGAGGAATTACATGCCGAAAGTTGGATCGTTCGGCCTGGACATGATGTTCCGCACATGCACGGTTCAG

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|7219950|gb|AU063307.2|AU063307
EST:     TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG                         GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
genomic: TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAGgtagttttgg ... ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
EST: gi|33796283|gb|CF324008.1|CF324008
EST:     TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG                         GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
genomic: TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAGgtagttttgg ... ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
EST: gi|58658531|gb|CK047211.1|CK047211
EST:     TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG                         GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
genomic: TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAGgtagttttgg ... ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
EST: gi|29679436|gb|CB675711.1|CB675711
EST:     TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG                         GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
genomic: TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAGgtagttttgg ... ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
EST: gi|29677970|gb|CB674245.1|CB674245
EST:     TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAG                         GGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG
genomic: TTGGTTTTCAGCCAAAGTGGGCACTGAGTGACATACCAATAATGCCCAAGgtagttttgg ... ttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacttacgagaagggttcctataaattttaatgcttcagattgtttctttatagGGAAGGTACGAAATTATGAGGAATTACATGCCTAAAGTTGGCTCTCTTGGGCTTGATATGATGTTCCGAACATGCACTGTTCAG
                                         ttgtttcttt  CT-rich tract
                ttcctataaattttaa  TA-rich tract