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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

Basic information

species Oryza sativa
transcript LOC_Os02g02840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G846811_T01 (Zea mays), 3'ss of exon 2
--------------------gtaatctggttgcgctgctatctaattctgcatgcttgttttcttc---taccaagtta-ttaagtttttccttcggaa-taccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
                    || |  | | |||  | |   |   || |||||     ||||| |    || |||  |  || |  ||   ||| | || | || ||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||| || ||||| ||||||||||||||||||||
gtgaccagctatcctattttgttactttgatgcttttcc-cccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAGGCCAGCTATGAGAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G803949_T02 (Zea mays), 3'ss of exon 2
-------------------------------------gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctacca----agttattaagtttt--tccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
                                      | ||    ||    | || ||   | |   ||     |||||||    ||    | |  || || ||   || ||   | |   | |||||| ||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| ||||| || ||||| || |||||||||||||||||
gtgactagccgtgctgttctgtcctgtcctgctacttatgatgctttttttttcctttcctttgcgcgatatcctttttctttgttcatcaaaatggttgagcttccatctttgcaactgtaatagGTCAAGAGGATTACAACAGACTGAGACCACTGAGCTATCGTGGAGCTGATGTTTTTCTTCTGGCTTTCTCACTGATCAGTAAAGCCAGCTATGAGAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G08380.1 (Glycine max), 3'ss of exon 3
gtaatctggttgcgctgctatct----aattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
|||||   |      |  | |||     ||  || |   | |   | ||||    | |||||  ||| ||  |  |||     ||||| || ||||||||||||||| | |||||  ||||||| ||||| || ||||||||| |  |||| ||||| || || ||||||||||| ||||| |||||
gtaatgctgcgtgattattgtctctgtgatgttggagcttggaagttttctctggatttattgtgttatt--tgtgga-----acagGACAAGAGGATTACAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATATTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G02540.2 (Glycine max), 3'ss of exon 2
gtaatc-tggttgcgctgctatctaattctgcatgcttgttttcttctaccaagttatta--------agtttttccttcggaatacc--acagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
|||||  ||    |    | |  ||  |     ||  | || | ||  || || | |||          ||||  | |   |  |     ||||||||||| ||||| || || || |||||  |||| ||||| ||||||||||||||  | || ||||| || || || |||||||| |||||||| ||| |
gtaattatgacaaccaatccacttatatagaattgggtattgtttttgacaaattgattgtttttggtggtttaacttcttgtttgattaacagGTCAGGAAGATTATAATAGGCTTAGACCCTTGAGCTATCGAGGAGCTGATGTTTTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G02580.2 (Glycine max), 3'ss of exon 2
--------gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaatacca-cagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
        |  | |   ||  | |  |||  |||   | ||  || ||  ||  |     |||  |     |||   | |    |  | |||||||||||||||| || || || |||||  |||||||||| ||||||||||| ||  | || ||||| || || || |||||||| |||||||| ||| |
gtaattatgacaaccaattcagtta-tatagaatcgggtattatttttgactaattgtttgtttctggtggtttaacttgtttgattaacagGTCAGGAGGATTATAATAGGCTTAGACCCTTGAGTTATCGAGGAGCTGATGTATTTATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G02530.3 (Glycine max), 3'ss of exon 2
-------------gtaatctggttgcgctgctatc--taattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
               |||    ||     | | ||  ||    |   ||| | || | |  | |  |    ||||  | ||  ||  || ||  |||||||||||||||||||| ||| | |||||  |||| ||||| ||||||||||| ||| | || ||||| || || || |||||||| |||||||| ||| |
gtaacatggcaaaacaattcaattatatagttttcagtatcattttctgcatattgtttgtttctgatggtttaacatattgttt--gatta--acagGTCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGAGCTGATGTCTTCATACTTGCCTTTTCTCTCATAAGCAAGGCTAGCTATGAAAATAT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G36880.1 (Glycine max), 3'ss of exon 3
gtaatctggttgcgctgctatct----aattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
|||||   |      |  | | |     ||  || |   | |   | ||||    | |||||  || || | |  |||     ||||| || |||||||| |||||| | |||||  ||||||| ||||| || ||||||||| | ||||| ||||| || || ||||||||||| ||||| |||||
gtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttatt--gtgttacttgtgga-----acagGACAAGAGGATTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCCGATGTTTTCATACTGGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G11510.1 (Glycine max), 3'ss of exon 2
gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctaccaa-gttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
||||     | |   | |    | ||  | ||| ||| || | || |   |  ||| |    || ||        ||  |||||| || || |||||||| ||| |||||||  | || ||||||||||| ||||| ||||| || || ||||| || || |||| |||||||||||| |||||
gtaagt--atagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacagGCCAAGAAGATTACAATAGATTGAGACCCTTAAGCTATCGTGGAGCAGATGTATTCCTGCTTGCTTTCTCTCTCATAAGCAGGGCCAGCTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G05160.1 (Glycine max), 3'ss of exon 2
gtaatctggttgcgctgc---tatctaattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
||| | | |||    |     | || | |   | ||| |   ||  || ||     ||||||  | | |  |  ||||||     ||||| |||||||| || ||| |  ||||  ||||||||||||| |||||||||||| |  | || ||||| || || ||||||||||| ||||| |||||
gtattgttgttattttttctttgtccattctgggatgttgagttctttttagatttttattat-tctattatgtggaata-----gGTCAAGAGGATTATAATAGATTACGACCTTTGAGTTATCGTGGTGCTGATGTTTTCATATTAGCTTTCTCTCTCATAAGCAAGGCCAGTTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G35950.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatctg-gttgcgctgctatctaattct--gcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
|||||    | ||  |   |   |||| ||  |   |   | |||| |  |  ||    |  |  || |  ||  |  |    |||| || ||||| || |||||| | |||||  ||||||| ||||| |||||||||||| |||| |||||||| || || || ||||| || |||||||||||
gtaatgaatgatgatccaattcataatccttggtgagagagctttccttgatgaatcggtcgaaattatgtttttggtttatgcagGGCAAGAGGACTATAACAGATTAAGACCTTTGAGTTACCGTGGTGCTGATGTTTTCATTCTTGCCTTCTCTCTCATTAGTAAGGCTAGTTATGAGAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G17800.2 (Arabidopsis thaliana), 3'ss of exon 3
------gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaatacca--cagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
         |  |  | | | |  ||  || |  |    |   | | |    |     | | | ||  ||||  || |   |   |  |||| ||||||||||| |||||| | |||||  ||||||| || || |||||||||||| |  | || ||||| || ||||| ||||| || |||||||||||
gtactgactaaataatagggatcttacttagtagta-gcggcagctatgggat-ttggggtctgaaacttttgttttgttgttgtaaacagGGCAGGAGGATTATAACAGATTAAGACCTTTGAGTTACCGCGGTGCTGATGTTTTCATCTTAGCATTCTCTCTTATCAGTAAGGCTAGTTATGAGAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 3'ss of exon 2
gtaatctggttg-cgctgctatctaattctgcatgctt------gttttcttctaccaagttattaagtttttcc-ttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
|||||||  |   |     | |  | ||||  || |||      |||| ||  |  |  ||| |||| |   |   ||||   |   ||||| |||||||||||||| ||| | |||||  |||| ||||| || ||||| |||||  |||| || ||||| || || ||||||||||||||||| |||||
gtaatcttatgaacatccttctggatttcttgattcttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacagGCCAGGAGGATTACAATAGATTAAGACCCTTGAGCTATCGAGGGGCTGACGTTTTTATTCTTGCATTCTCTCTCATTAGCAAGGCCAGCTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 3'ss of exon 3
-----------gtaatctggttgcgctgctatct--aattctgcatgcttgttttc-ttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
           || |  || || |  |  | | |  ||||    |      ||||  || |   | |    | | ||| | ||      |   ||||| |||||||||||||||||| |||||||  |||||||||| || || ||||||||| |  |||| ||||| || |||||||||||||||||||| |||||
gtagcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctt---tggaacagGGCAGGAGGATTACAACAGATTGAGACCTTTGAGTTATCGCGGGGCAGATGTTTTCATATTGGCATTCTCTCTCATCAGCAAGGCCAGCTATGAAAATGT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S126_126V6.2 (Physcomitrella patens), 3'ss of exon 3
-----------gtaatctggttgcg--ctgctatct-aattctgcatgcttgttttcttctac-caagttattaagtttttccttcggaatacca--cagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
            | ||       |   || | ||   || ||  |    | ||| | |  ||  | | || | |       | ||    |  | |  ||||||| || ||||||||||||||  |||| ||||||||  | || ||||||||||| ||||| || || || || ||||||||||| || ||||| ||| |
ttttggtcttgctgattcacacacaaccttccattggaagtcgaccccttagttatttcttattccatttgtcactgaaaacatttactaccctatgcagGTCAAGAAGATTACAACAGACTTCGACCTCTGAGTTACAGAGGCGCTGATGTTTTTCTTCTAGCATTTTCTCTTATCAGCAAGGCTAGTTATGAAAATAT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------gta-atctggttg--cgctgctatctaattctgcatgcttgttttcttctac--caagttatt--aagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
             | | ||  |||    | |||     || |  |   ||  || | || |  ||  || || |||  ||    |||   | || |    ||||||| || ||||||||||| ||  | || ||||||||  | || ||||||||||| || ||||| ||||| || ||||||||||| || ||||| ||  |
tggtccaacagctgcacatacggtcattcactgtacggtattcatctttgggtgatatcattcacttcatgtcattgaaaacaattcgccctgatt---gcagGTCAAGAAGATTACAACAGGCTTCGTCCTCTGAGTTACAGGGGTGCTGATGTTTTTCTCCTGGCGTTCTCCCTCATCAGCAAGGCTAGTTATGAAAACAT

upper sequence: LOC_Os02g02840.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ11645 (Selaginella moellendorffii), 3'ss of exon 2
gtaatctggttgcgctgctatctaattctgcatgcttgttttctt--ctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
                |  |   ||   |   || ||| |||       |   | |   | |  | |  || |    |  | ||||||| || ||||||||| |  |||| || || || ||| | ||||| |||||||||||  ||||||| || || ||||||| |||||||||||| ||  |
------------gttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATGTTTTCCTCTTGGCCTTTTCCCTTATCAGCAGGGCCAGCTATGAAAACAT

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|88406526|gb|CI599019.1|CI599019
EST:     CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG                         GTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATG
genomic: CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggt ... aataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATG
EST: gi|33683752|gb|CF311991.1|CF311991
EST:     CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG                         GTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATG
genomic: CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggt ... aataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATG
EST: gi|88405462|gb|CI588668.1|CI588668
EST:     GGTCGTGGTTGATGGTAAAACCGTCAACCTCGGGCTATGGGACACTGCAG                         GTCAGGAGGATTACAACAGACTGAGACCAATGAGTTATCGTGGAGCTGATG
genomic: CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggt ... aataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATG
EST: gi|88414951|gb|CI601783.1|CI601783
EST:     CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAG                         GTCAGGAGGATTACAACCAGACTGAGACCACTGAGTTATCGTGGAGCTGAT
genomic: CGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggt ... aataccacagGTCAGGAGGATTACAAC-AGACTGAGACCACTGAGTTATCGTGGAGCTGAT

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: 66 (upstream exon), 65 (downstream exon)
Score: 53

GATTATGTTCCGACGGTGTTTGACAACTTCAGTGCCAACGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggt ... aataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT
                      aagttattaagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctggttgcgctgctatctaattctgcatgcttgttttcttctaccaagttattaagtttttccttcggaataccacagGTCAGGAGGATTACAACAGACTGAGACCACTGAGTTATCGTGGAGCTGATGTTTTCCTTCTGGCCTTCTCGCTAATCAGCAAGGCCAGCTATGAGAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG