Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctaaaacagctctgtcgattagagaaggcataataagttattgcttcgatgtgtttgacacacttttttttaccataatttgttttattttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGATAGCCAGATA

Basic information

species Oryza sativa
transcript LOC_Os02g08480.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G037185_T01 (Zea mays), 3'ss of exon 8
--------tctaaaacagctctgtcgattagagaaggcata-ataagttattgcttcgatgtgtttgacacacttttttttaccataatttgttttattttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGA-TAGCCAGATA--
        | || || |  |    |   | |||      || | | | ||| |    |||    ||     |||     ||    |    | ||  |||     ||||||  |||||||||||| |  |||||   ||||||||||| || || |||||| |||| || ||||||| |||||||||| ||||||||||| ||   ||  |  
gttggtcttttacaatattttgagctcgttgagtccatctacacatgatatggaagtgattaccttatggaactacgccttgatgttccattttgcattaaatgtgtagGCACCTGAAAAGGAAGCAGAGGAG---CCCAAGAAAGAAGACCCAAAATTCGCAGCATTCACAGGAAAGAAATACTCACTGAAGGGCTGAATAAATAGGAAGA
















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|86873388|gb|CI341613.1|CI341613
EST:     AGGTTGTTTTTGGCCCTGCTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|27921103|gb|CB096911.1|CB096911
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86425429|gb|CI070526.1|CI070526
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|29641787|gb|CB646794.1|CB646794
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86414416|gb|CI068819.1|CI068819
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86837102|gb|CI347616.1|CI347616
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|89191945|gb|CI250886.1|CI250886
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86425876|gb|CI070973.1|CI070973
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|29641788|gb|CB646795.1|CB646795
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|89175161|gb|CI111680.1|CI111680
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88961112|gb|CI096515.1|CI096515
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88510728|gb|CI438234.1|CI438234
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|87018863|gb|CI256748.1|CI256748
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAGCAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86833083|gb|CI333682.1|CI333682
EST:     AGCTTGTTTTTGCCCCTGGTGGGAACCCCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAATAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88225329|gb|CI225245.1|CI225245
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88222206|gb|CI222162.1|CI222162
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88490808|gb|CI428080.1|CI428080
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86527163|gb|CI167369.1|CI167369
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88249019|gb|CI248868.1|CI248868
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88443453|gb|CI552196.1|CI552196
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88248256|gb|CI248105.1|CI248105
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|29663476|gb|CB659751.1|CB659751
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|87018867|gb|CI256752.1|CI256752
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAGCAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|88484133|gb|CI421404.1|CI421404
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86492083|gb|CI134716.1|CI134716
EST:     AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
EST: gi|86487488|gb|CI130121.1|CI130121
EST:     AGCTTGTTTTTGGCTCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAG                         GTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC
genomic: AGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTC

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: 73 (upstream exon), 69 (downstream exon)
Score: 71

CTCAACAGCGTCCACATCACAGAGCAGTTCATCTCGTAAAACCACGGAAAAGCTTGTTTTTGGCCCTGGTGGGAACCGCACATCTAAGGAAACAGAAAAGgttggtattt ... ttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGATAGCCAGATA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatgtgtttgacacacttttttttaccataatttgttttattttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGATAGCCAGATA
        gtttgac  putative branch site (score: 71)
                                  tttgttttattttc  putative PPT
                   ttttttttaccataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctaaaacagctctgtcgattagagaaggcataataagttattgcttcgatgtgtttgacacacttttttttaccataatttgttttattttcaatgtagGTGCCTGAAAAGGAACCGAAGGAGGATCCCAAGAAAGATGAACCGAAATTCTCAGCTTTTACAGGAAGGAAATACTCATTGAAGGGCTGATAGCCAGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
-ctaaaac
- - - - - - - - - - - - - - - - - - - - -ttgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtttga