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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatcttccagactgatgtttgtacttacaataaattgcaacctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA

Basic information

species Oryza sativa
transcript LOC_Os03g01810.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G042552_T02 (Zea mays), 3'ss of exon 3
ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatcttccagactgat--gtttgtacttacaataaattgcaac--ctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
     | |      || |   ||  | | | |     |||   |  | |||  ||  ||       |||||| |||||||  ||  |   |  | | ||||||||||| || ||||| || ||||| || |||||||| ||||| |||||||||||||||||   ||| |||||||| || ||||| || ||||| ||||||||
----cactcataagtgcaatatagtaatcgcagtatgattgtatgaaacttagaggttgtacaagctgtactgacaataagctgggaataccgtaatctttcagCTACAGCTAGGACAGTAGGCCACTTGTCCAAGAGCACTGAAGTGATGAAACTTGTCAACGGCCTCATGAAAGCCCCCGAGGTCGCAGCCACAATGCAGGA

upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 4
ctcatattacattttg--tagagtatcatttgtaagtgtattcctttcatcttccagactgatgtttgtacttacaataaattgcaacct--atcaccttt-cagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
 |  | ||| || |    |    |   ||| || |  |  ||   ||  | ||    |  ||  ||||| |||   | || |  |||| |   |    ||| |||| | |||  | || || || ||| |||| |||||| ||||||| |||||||||||||| ||||| | |||||| || ||  ||||||   | ||||| ||
-ttgtcttagatgtgaactcttttgcaattagtcatcgagttggatttgtgtt---aatagaattttgttctt-tgagaattaacaacttttgttgtttttgcagCAATTGCTCGTACGGTGGGACATCTATCAAAGAGTGCTGAGGTCATGAAACTTGTCAACAACCTCACGAAAGCTCCTGAAATGGCTGTGGCAATGCAAGA

upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G21900.1 (Glycine max), 3'ss of exon 3
ctcatattac-attttgtagagtatcatttgtaagtgtattcctttcatcttccagactgatgtttgtactt--acaataaattgcaacctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
    ||  || |  ||  |   |||  ||   ||||   |   |   |   |||| |  ||| ||||| |||    ||| |||  |      |    || |||| | |||  | ||||| || ||| |||| |||||| ||||||| ||||||||||||||||| || ||||| || || ||  |||| |  || ||||| ||
aatctacaactaccttacattttattcttctaaagtaactaaat---aaaatccataaagatttttgttctttggaaattaatgactttggttgtttttgcagCAATTGCTCGTACTGTGGGACATCTATCAAAGAGTGCTGAGGTTATGAAACTTGTCAATAATCTCATGAAGGCTCCCGAAATGGCGGTGACAATGCAAGA

upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 4
ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatcttccagactgatgtttgtacttacaataa--attgcaacctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
    | |  | | ||     | ||| |    |||  |  | |||   | ||    | |  | |   | |||  | |    || |       | |  ||||||| | |||  | || || || ||||| || |||||| | ||||| ||||||||||| |||||||| ||||| || || || ||||||| ||| ||||| ||
--tttctagcttgttactttgaatcctcaagaaggcttctgcttaactgttttgaatttctatggattcttgaactcctcatggttttggttgatttttcagCAATTGCTCGTACGGTGGGGCATTTGTCGAAGAGTGCAGAGGTAATGAAACTTGTTAATAACCTCATGAAGGCTCCTGAAGTGGCTGTCACGATGCAAGA

upper sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S104_29V6.1 (Physcomitrella patens), 3'ss of exon 3
ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatct--tccagactgatgtttgta-----cttacaataaattgcaacctat-cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
         || ||  ||  |  |  |    |  |      ||    |    | |||  |  ||  ||||      ||   |   ||||     ||| |  ||| |||| || || ||| | || || ||  |    || || ||||| || ||||||||||| || ||||| |||||||| || || ||||| ||||||||||| ||
--------ccaattgttaatgggttgtcaacagattggcatctgatgttcgatgcaggatagtgactgtaatggttttctgactgattgttgtgtattcgacttgcagCCACGGCGAGGGCGGTAGGGCAACTGCAGAAAAGCACTGAAGTTATGAAACTTGTAAACAACCTCATGAAAGCTCCTGAAGTGGCAGCCACCATGCAAGA

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|27547715|gb|CA767395.2|CA767395
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
EST: gi|95101417|gb|CI693165.1|CI693165
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGAC
EST: gi|88310672|gb|CI672535.1|CI672535
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
EST: gi|27576250|gb|CA998944.1|CA998944
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAA
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAA
EST: gi|58686936|gb|CK075623.1|CK075623
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
EST: gi|88587132|gb|CI704860.1|CI704860
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGA
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGA
EST: gi|88382928|gb|CI683023.1|CI683023
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTG
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTG
EST: gi|88408489|gb|CI685983.1|CI685983
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGGAGTAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAG-AGTAC
EST: gi|112785790|gb|EE591423.1|EE591423
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
EST: gi|33666695|gb|CF297662.1|CF297662
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAAC
EST: gi|88580269|gb|CI697183.1|CI697183
EST:     GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAG                         CTACTGCCAGGACTGTTGGCCATTTATCC
genomic: GAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCC

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: 68 (upstream exon), 74 (downstream exon)
Score: 14

CTGGCCAAGGAGGTGGTGAGGTCCAGGAAGGCGGTCAACCGCCTCTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAGATCGTAGgtaacgaatc ... cacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catcttccagactgatgtttgtacttacaataaattgcaacctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA
                     tacttac  putative branch site (score: 14)
                                            tcacctttc  putative PPT
                     tacttacaataaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcatattacattttgtagagtatcatttgtaagtgtattcctttcatcttccagactgatgtttgtacttacaataaattgcaacctatcacctttcagCTACTGCCAGGACTGTTGGCCATTTATCCAAGAGTACTGAGGTGATGAAACTTGTCAATAACCTTATGAAAGCACCAGAGGTGGCTGCCACCATGCAGGA

- - - - - - - - - - - -tcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaacc