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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcttgctcagttcttaatgattttttacctccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG

Basic information

species Oryza sativa
transcript LOC_Os04g40040.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 6
--gtgcttgctcagttcttaatg---attttttacctccagagagttttaactttcatctgactattatatgcctttttttt-tgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
      ||  ||||||||| |||   ||  |||  |     | | ||||  |||| || |||||||  | |      ||||| || ||||||| || || || || | |||||| |||||||||||||| ||||| || || || ||||||||||| ||||||||||| ||||| |||||||||||||
gttattttattcagttcttgatgtgtatactttgacgttcaaaattttt--ctttgatttgactatgctctttaacctttttgtgcagGGATGCGATTGCTTGGGCTACATAAAATATTTTGATGCACATTTCACAAACTTCACTGGTGGTGTGGAGACAATTGAGAACTGTGTTTGTTTGCATGAGG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 6
---------------gtgcttgctcagttcttaatgattttttacc---tccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
                || |  ||    |  | || |||| | |||   | |     | ||  | |    | |  ||    |     ||| || ||  |||||||||| ||||| || | ||| |||||||||||||| |||||||| ||||| || ||||| |||||||||||||| |||||||||||||||||||| |
gtattagaataatatttgttctcttgtatgcttatcatttgtcaccgtattctttctgattggattcctttttatctgaggttaatgtttgttgttacagGGATGTGATTGTTTGGGATACATCAAGTATTTTGATGCTCACTTCACAAATTTCACTGGTGGGGTGGAAACAATTGAAAATTGTGTATGTTTGCATGAAG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G04360.1 (Glycine max), 3'ss of exon 6
-------------gtgcttgctcagttcttaatgattttt-tacctccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
              | ||   | |||    ||| | | |  |  ||| |   || |  ||||   || |   | ||   ||      || ||| |||| ||||| |||||||| |  || ||||| |||||||| |||||||| || ||||  || ||||| |||||||| ||||||||||| || |||||||| |
gtcaaggcattttcttctaatttagtctcaaattactctcctttctctatgtagatgaaactaaaattta--ttttgcttggtgacattattgcagGGTTGTGATTGTTTAGGCTATATCAAGTACTTTGATGCTCACTTCACAAACTTTAATGGAGGTGTTGAAACAATAGAGAATTGTGTTTGCTTGCATGAAG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA17G09290.1 (Glycine max), 3'ss of exon 5
-------gtgcttgc-tcagttcttaatgattttttacctccagagagttttaactttcatctgactatta-tatgcct--------ttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
          | |   |   | |||    || |||||  |  |   ||||     ||     | | | | | |  | ||          ||| ||| |||| ||||| ||||| || | ||| || || |||||||| || ||||| ||||| || ||||| || || |||||||| |||||||||||||||||||| |
gtttgagaaacctatatttatccttttcaatgttttatatttaccaagttcctctttctgattaagtttcaatgagtctaaagtcaacatttgttgcagGGGTGTGATTGTTTGGGCTACATCAAATACTTTGATGCTCATTTCACAAATTTCACTGGTGGAGTTGAGACAATTGAAAATTGTGTATGTTTGCATGAAG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G20800.1 (Glycine max), 3'ss of exon 6
-----gtgcttgctcagttcttaatgattttttacctccagagagttttaactttca-tctgact---attatatgcctttt-----------tttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG-
     |   ||||| |  |   |   ||| ||   || ||    |  |    | ||| | | | |   |||  ||   ||||            | ||  |||| || || |||||||| |  || || || |||||||| |||||||| || ||    || ||||| |||||||||||||| ||||| ||||||||||| | 
taaatgcatttgcttatattccagacattctt-gtcttcattttgcctcctttctcaatgtaaatgaaattgaatttgttttgcataatgtgactgtttcaggGCTGCGATTGTTTAGGCTATATCAAATACTTTGATGCGCACTTCACAAACTTCTATGGAGGTGTTGAAACAATTGAGAACTGTGTTTGTTTGCATGAAGA

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv00s0225g00090.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------gtgcttgctcagttcttaatgattttttacctccagagagttttaactttcatctgactattatatgcctttttttttgt-----agGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
                                     | ||      ||| |||   |||  |||| ||  |  | |  |||   |  | |   | || | ||    | | | |||     |||| ||||| || ||||| |  || ||||| ||||| ||||| || || ||||| || |||||| | ||||||||||| |||||||| || |||||||| |
gttagagtgcttactcctatgctgattttctttgtattactattgttgttgttatatattagttacatcaggctaatcataatgatttttttttttttttttggtcatgtctgtgtggtgcagGGCTGTGATTGCTTAGGATATATCAAGTACTTTGACGCACATTTTACAAATTTCACTGGTGGTATCGAAACAATTGAAAATTGTGTTTGCTTGCATGAAG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 6
----------------------------gtgcttg---ctcagtt--cttaatgattttttacctccaga-gagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
                            || |||     | | ||  | |  ||    |||||        || | | ||   || |||| || | | |||   || |      |||||||||| ||| |||| || || || || |||||||| ||||| || || || || || ||||| ||||| ||||| |||||||| ||||||||||| |
gtctataaaactatttcttcatgtaattgtccttaaattttattttaccttgtggaactttactattgtttgaatctaaaagatcttctg-ctttaaaatgaaattatgaccacagGGATGTGATTGTCTAGGGTTTATCAAATACTTTGATGCCCACTTTACAAACTTCACTGGAGGTGTTGAAACGATTGAAAATTGTGTTTGTTTGCATGAAG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S36_16V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------gtgcttgctcagttctta-atgattttttac-ctccagagagttttaactt-tcatctgactattatatgccttttt--ttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
                       |||  |  |||| |   |  | | |||| |   || | | |  |   | |  | |    |  | |  | || |    | || |||| ||||| ||| | ||   ||||||||| || || || |||||||||||||||  ||| |||||||| ||||| ||||||||||| ||| |||||||||
gtgaatgattctcacaacgttcacttcttgggttcatgtgttctatcttacgcaatagtgcgatcaagtctgttgtattgacaaaacaaacgttgtgaactctgcagGGTTGTGATTGTCTTGGCCACATAAAGTACTTCGACGCTCACTTCACGAATTTTCTGGGAGGTGTGGAGACAATAGAGAATTGTGTGTGTATGCATGAGG

upper sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S26_107V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------gtgcttg----ctcagttcttaatgattttttac--ctccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
               ||  |||     | | ||   |  | ||  | ||  |||  | ||   ||| ||    | ||||     ||   ||    || || |||| ||||| ||| | ||   ||| ||||| || || || |||||||| ||||||  ||| |||||||| ||||| ||||||||||||||| |||| ||||
gtgagtggttttgacgtagttgaggctttaatttacagggtttaatgactactcttgcgaacatta-ctaatttatgac-gcgctacctctgagcttctgcagGGTTGTGATTGTCTCGGCCACATTAAGTACTTCGACGCTCACTTCACAAATTTTCTGGGAGGTGTGGAGACAATAGAGAATTGTGTATGTATGCACGAGG

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|88410479|gb|CI686413.1|CI686413
EST:     TCGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|29673126|gb|CB669401.1|CB669401
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|11442746|gb|BF430649.1|BF430649
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|58690279|gb|CK078966.1|CK078966
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|58690776|gb|CK079463.1|CK079463
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|428641|gb|D24793.1|D24793
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGNAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|33812562|gb|CF332169.1|CF332169
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|88348489|gb|CI629978.1|CI629978
EST:     TGATGCTGGAGAAGATGGACTTGCGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTCCATAAAGTATTTCGATGCACACTTCACCAAT
genomic: TGATGCTGGAGAAGATGGACTTG-GGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|29675868|gb|CB672143.1|CB672143
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|88592151|gb|CI710233.1|CI710233
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT
EST: gi|88337375|gb|CI629665.1|CI629665
EST:     TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGG                         GGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCAAGAAT
genomic: TTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 75 (downstream exon)
Score: 33

GGTTGTTCCTTATGGAGATCCCAATGAACCACATTATCGCAAGAATGCTTTTGATGCTGGAGAAGATGGACTTGGGAAGAATGCTCATTCTCTTAAGAGGgtgcttgctc ... ttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctccagagagttttaactttcatctgactattatatgcctttttttttgtagGGATGTGACTGTTTAGGTTTCATAAAGTATTTTGATGCACACTTCACGAATTTTACGGGTGGTGTGGAAACAATTGAGAATTGTGTATGTTTGCATGAGG
                                    tatgccttttttttt  CT-rich tract
                                          tttttttttgta  TA-rich tract