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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgctatgctgaaatctgaacaatctagtactactagagt...

Basic information

species Oryza sativa
transcript LOC_Os02g13530.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G091383_T01 (Zea mays), 5'ss of exon 2
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctct--cttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgc-tatgctgaaatctgaacaatctagtactactagagt-
|||||||||||||||||| |||||||| ||||||||||| ||||||||||||||| ||||| | |||||||||| |||||||||||||||||| ||||||||| ||| |||| || || |||| |||| | | | ||| | || | | || || ||| ||| | | | || | | | |
CCGCACCCACTTCGGAGGCGGCAAGTCTACCGGATTCGGTCTCATCTACGACAACGTCGACTCAGCCAAGAAGTTCGAGCCCAAGTACAGGCTTATCAGGgtatgcgtctcttgctcctcccgtttttctcactcgtaattggattcataggtct--ccatgttgaatatactg--cctggtatacgctgaaagctcaaagctt

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G37190.1 (Glycine max), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgc---tatgctgaaatctgaacaatctagtactactagagt
|| || || || || || ||||||||||| || || || | ||||| || | || ||||||||||||||||| ||||||||||| |||||||| | | | ||| || || | | || || || | |||| | | | ||| || || | ||
TCGAACTCATTTTGGTGGTGGCAAGTCCACTGGGTTTGGTTTGATCTATGATTCAGTTGAGAATGCCAAGAAGTACGAGCCTAAGTACAGGCTTATCAGGgt--gagttatttaaatctttctgtgtcaattatgattataatttttcccctttgttaaaatgccttttttttttaattagacgggctgtttataaataata-

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA19G43190.1 (Glycine max), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgctatgctg---aaatctgaacaatctagtactactagagt
||| || || || ||||| ||||| ||||| ||||| || | || || || | | || ||||||||||| |||||||| |||||||| |||||||| | | | || | | | | | || | | | | | | | | |||| | | || | ||| || | ||| || |
CCGAACACATTTTGGAGGTGGCAAATCCACTGGATTTGGTTTGATTTATGATACAGTGGAGAATGCCAAGAAGTATGAGCCCAAATACAGGCTTATCAGGgtcagt-caacaattaacacaacctctgcttgtttttttttacaatctgaaatcacatttgttttatggtatttagatttttacagtcctgcactccttgc--

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0030g01620.t01 (Vitis vinifera), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgc-------gcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgc-tatgctgaaatctgaacaatctagtactactagagt
||| || ||||| ||||| || ||||| || ||||| || | || || || | || || |||||||||||||| ||||||||||||||||||||| |||| || ||||| || | || || || || | | || | | || | | |||| || |
CCGGACTCACTTTGGAGGTGGGAAGTCTACTGGATTTGGTTTGATTTATGATTCAGTTGAGAATGCGAAGAAGTACGAGCCTAAGTACAGGCTCATCAGGgtaaattatataaatctctttttctcatttgatttcatcaagcatcaagctattctgtatatgagggttgtgcgtttttgtatttagatgatctt-tattt-------

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP07861 (Chlamydomonas reinhardtii), 5'ss of exon 4
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgctatgctgaaatctgaacaatctagtactactagagt------
||||| || |||||||| ||||| || || ||||||||||| |||| | ||||||||| ||| ||||||||||||| | ||| ||||||| |||| || | | | || | | | | | | ||| || | |||| | | | | | |||
----------TTCGGTGGTGGCAAGTCGACCGGCTTTGGCCTCATCTACGATGACCTGAAGGCCGCCAAGCAGTTCGAGCCCAAGTACCGCCTCGTCAGGgtgagcgcg-ctgctatataaatg-tactgtaggatttccagtcgcaggaaccagcggtg--gcgaggctgtggatgcagt--cttggagccgatggagcaggcgg

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S450_9V6.1 (Physcomitrella patens), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgt-tgatctcgccctgctcttgatagtttag--tttaatcg----tgatgctatgctgaaat--ctgaacaatctagtactactagagt-----------------------------------
| | ||||| || ||||| ||||||||||| |||||||| ||||||||||| | ||| | |||||||| |||||||| |||||||| | |||||||| | | || | || | || | | || | | ||| | || | | || ||| || || | || | || ||
CAGGACCCAGTTTGGAGGTGGCAAGTCCACTGGATTCGGTCTCATCTACGATTCTGTTGACTCTGCCAAGAAATACGAGCCGAAGTACAGATTGATCAGGgtgagttttctgtctccatcatgtggagtgcttatggtgtcgaggagtgaaaatttgagcggtctcggcttttctcttgaatggctacacgcttaggttgtctcagtgttaagtattgaaattttgggtgttggggatgtgcag

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S204_49V6.1 (Physcomitrella patens), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctct--cttgtctcgttgatctcgccct---gctcttgatagtttagtttaatcgtgatgctatgctgaaatctgaacaatctagtactactagagt-------------
| | ||||| || ||||| ||||||||||| ||||| || |||||||| ||| ||||| | ||||| || |||||||| ||||||||||| || |||||| | | || | | | || || | | | | | ||| ||| | | || | | | || ||||| || || | ||| | | |
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGATTTGGCCTCATCTATGACTCTGTCGACTCTGCCAAAAAATACGAGCCTAAGTACAGGCTTATTAGGgtatgtgtttccaccccttactgatgcccttgttgttacgtccctcata-tttcataatacagtactaatggtcgcaattctgagcattccatgacttcatgcatttgcgaattgtag

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S13_236V6.1 (Physcomitrella patens), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtg--atgctatgctgaaatctgaacaatctagt-actactagagt------------------------------------------------------
| | || || |||||||| ||||||||||| ||||| || |||||||||||| | | ||| | || ||||| ||||||||||||||||||||||| ||||| | | || ||| | || || ||||| || | | | || | ||| ||| | | || ||| | | | | | ||
CAGAACGCATTTCGGAGGTGGCAAGTCCACTGGATTTGGTCTCATCTACGACTCCATTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtgagattcatcgagacctgattggt-tcatccggctct-gaggttcttgaaaggtcaaggcatgttatttttttgttgaaataatttgctgattggtttggtgtgttcatttgtcaagatctttagtattgaggatagtttaatggttatttgcag

upper sequence: LOC_Os02g13530.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S37_112V6.1 (Physcomitrella patens), 5'ss of exon 3
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttg-atctcg----ccctgctcttgatagttta--gtttaa--------tcgtgatgctatgctgaaatctgaacaatctagtactac-tagagt-----------------------------------
| | ||||| || ||||| ||||||||||| || ||||| || ||||||||| | ||| | || ||||| ||||||||||||||||||||||| |||||| | || ||| | | | | || || |||| ||||| | || | ||| || || || ||| | ||| || ||| | || | | | |
CAGGACCCAATTTGGAGGTGGCAAGTCCACTGGGTTCGGTCTTATCTACGACTCTGTTGACTCTGCTAAGAAATACGAGCCCAAGTACAGGCTCATTAGGgtatgt-tctgtctcggcgcagggtgtcacgggatttctgcgagtgataatctatagcttatgctacctttctcaatttcattctggcaatcgaa-aacctaattctgcatccactgtaattttaataactttcaaattgggaacatgtag

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|89165150|gb|CI255207.1|CI255207
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|87031413|gb|CI261787.1|CI261787
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|88213743|gb|CI213592.1|CI213592
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|55411479|gb|CV723855.1|CV723855
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|427216|gb|D23298.1|D23298
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|87007097|gb|CI277172.1|CI277172
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCTCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|88558939|gb|CI489471.1|CI489471
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTTTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|87011719|gb|CI281421.1|CI281421
EST:     GTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGTTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: GTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|86416175|gb|CI030186.1|CI030186
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|3762404|gb|C99652.1|C99652
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|86510587|gb|CI153220.1|CI153220
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|88208253|gb|CI208102.1|CI208102
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|88524829|gb|CI453780.1|CI453780
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|38471297|gb|CF955428.1|CF955428
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|86420572|gb|CI056561.1|CI056561
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|88242685|gb|CI242534.1|CI242534
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|8336460|gb|BE040907.1|BE040907
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAAG                         AATGGCCTCGCCACCAAAGTTGAGAAAGTCTCGCAAGCAGATGAAGGAGAG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAA-GTCTCGCAAGCAGATGAAGGAGAG
EST: gi|88241783|gb|CI241632.1|CI241632
EST:     ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
EST: gi|87022540|gb|CI267677.1|CI267677
EST:     ACGACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGG                         AATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG
genomic: ACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGG

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: 75 (upstream exon), 72 (downstream exon)
Score: 147

CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcct ... atacctacagAATGGCCTCGCCACCAAGGTTGAGAAGTCTCGCAAGCAGATGAAGGAGAGGAAGAACAGAGCAAAGAAGATCCGTGGTGTGAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCACCCACTTCGGAGGAGGCAAGTCCACCGGATTCGGACTCATCTACGACAACCTCGACGCCGCCAAGAAGTACGAGCCCAAGTACAGGCTCATCAGGgtacgcgcctctcttgtctcgttgatctcgccctgctcttgatagtttagtttaatcgtgatgctatgctgaaatctgaacaatctagtactactagagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcgccc