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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcccatcttaccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtctacttccag

Basic information

species Oryza sativa
transcript LOC_Os01g68320.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G059020_T01 (Zea mays), 5'ss of exon 6
CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc-catct---taccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtc-----tacttccag
                                         |||||| ||| |||||||||| ||||||||||| ||||||||||| |||||||| |||||||  ||  | |||||    ||   || |  |||| ||   || |  || ||  || | |   ||  |||      ||||  ||
-----------------------------------------AAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGACCTTAGAAGAGgtacctgcacacatctgtccactttaattctttttagatg-aatgccttttaaactcaatgcattctgtcatttgcacttttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G362850_T01 (Zea mays), 5'ss of exon 5
CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc-catct---taccgaaaataattttggacataaggttttgtaggctaa----gtctcttgcgtctacttccag
||  ||||||||   |||||||||||||| ||||||||||||||||| ||| |||||||||| ||||||||||| ||||||||||| |||||||| |||||||  ||  | |||||    ||   || |  |||| ||   | |  |||  |    ||     ||| |    |  ||||  ||
CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGACCTTAGAAGAGgtacctgcacacatctgtccactttaattctttttagatgaatgccttttaaactcaatgcaatctgtcatttgcacttttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 4
lower sequence: AC209019.3_FGT003 (Zea mays), 5'ss of exon 2
CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc-catct---taccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtc-----tacttccag
||  ||||||||   |||||||||||||| ||||||||||||||||| ||| |||||||||| ||||||||||| ||||||||||| | |||||| |||||||  ||  | |||||    ||   || |  |||| ||   || |  || ||  || | |   ||  |||      ||||  ||
CAGGAAGAATCTACAAAATTTGGATCATATTCAAGAACTAGAAGCACATGTGTCTATGGTGGTGCACCTAAGGGTCCACAAATACGGGGCCTTAGAAGAGgtacctgcacacatctgtccactttaattctttttagatg-aatgccttttaaactcaatgcattctgtcatttgcacttttag

upper sequence: LOC_Os01g68320.3 (Oryza sativa), 5'ss of exon 4
lower sequence: AT5G63120.1 (Arabidopsis thaliana), 5'ss of exon 4
CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtattt-gtcccatcttaccgaaaat---aattttggac-----ataaggttttgtaggctaagtctcttgcgtctacttccag
||| | |||||  | ||||| || |     ||  |   |||||| ||||||||||||||||| || ||||| ||||| || || ||||| ||||| ||||||||||  |    |  ||  | |  |   |  | |||       ||      |   ||  || |  || ||  |    |  |||
CAAGAGGAATCAAGGAAATTCGGGTTGAGGTCTGGTGTTAGAAGTACTTGTATCTATGGTGGTGCTCCTAAAGGACCTCAGATTCGTGATCTTAGAAGAGgtattttattttttaatagtgtagttttcatgtctggttcttggatggaacatcaaagtttatgaatcatgattggcttgtcag

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|87023569|gb|CI286320.1|CI286320
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGTTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|66920314|gb|CX107162.1|CX107162
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29636635|gb|CB641644.1|CB641644
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29673236|gb|CB669511.1|CB669511
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29640324|gb|CB645333.1|CB645333
EST:     GGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: GGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29664446|gb|CB660721.1|CB660721
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29679220|gb|CB675495.1|CB675495
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29644134|gb|CB649141.1|CB649141
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|33797128|gb|CF324429.1|CF324429
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29638139|gb|CB643148.1|CB643148
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|33676329|gb|CF304568.1|CF304568
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|33801394|gb|CF326568.1|CF326568
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29675369|gb|CB671644.1|CB671644
EST:     ACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCT-GTCGGGTTGATCGATATGCTGGAA
genomic: ACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTC-GGTTGATCGATATGCTGGAA
EST: gi|218485924|gb|FG959170.1|FG959170
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29661777|gb|CB658052.1|CB658052
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29675371|gb|CB671646.1|CB671646
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29645557|gb|CB650564.1|CB650564
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29678103|gb|CB674378.1|CB674378
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29677571|gb|CB673846.1|CB673846
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29669296|gb|CB665571.1|CB665571
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
EST: gi|29667787|gb|CB664062.1|CB664062
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGG-TGAGATTTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAA
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGA-TTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAA
EST: gi|29670396|gb|CB666671.1|CB666671
EST:     TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAG                         GGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG
genomic: TATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAG

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), 74 (downstream exon)
Score: 98

CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcc ... ctacttccagGGGTTGAGATTGTCATTGCAACACCTGGTCGGTTGATCGATATGCTGGAAGGTGGTCACACTAACCTGCGAAGAGTAACATACCTCGTCCTGGATGAGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACAAGAATCTGGCAAATTTGGATCATACTCAAGAACTAGAAGCACTTGTATCTATGGTGGAGCACCTAAGGGACCACAAATACGTGACCTTAGGAGAGgtatttgtcccatcttaccgaaaataattttggacataaggttttgtaggctaagtctcttgcgtctacttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA