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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT

Basic information

species Oryza sativa
transcript LOC_Os02g12794.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G029559_T02 (Zea mays), 3'ss of exon 7
ttatatctctttgattaccattatttg-tcatctgctcccaacttctgttgtgtatgaagttctgtg---aattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
       | |       ||||||   | |  ||          || || | |||  | ||| || ||   || | |||| |||    || |    |  || ||||||||||||| |||||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||||| ||||| || ||||| |||||||||||
----gcatttaaacaccccattaagcggttctcaaagttttgtttttgatctgttagtagtgctatgcacaagtcaactgaactcaactcccatgtattttcagGTTTCTGGGACATGTATGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGACGAGAACACAGTGTCGTTTGTGACTATGAACAAGGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G134582_T01 (Zea mays), 3'ss of exon 7
-----ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattga---actcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
      ||||||| |||| |         || | | | | ||| || || || | |||  | ||| |  || |   |   ||| |||      |||||  ||||  |||||||||||||||||| |||||||| || |||||||||||||| ||||||||||| |||||||| |||||||| ||||| || |||||||||||||||||
gtttggtatatctttttggtg--------ttttaagcagttcctaagttttgatctgtcagtagtgcaatgtacgaaccaactgaactcaaactctcatgtattttagGTTTCTGGGATATGTACGACCCAGAGGGCTACTCCCTGTGGTTCTGTGACTACAAGTACAATGATGAGAACACAGTGTCGTTTGTGACCATGAACAAGGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G09640.1 (Arabidopsis thaliana), 3'ss of exon 7
----------ttatatctctttgattaccatta----tttgtcatctgctcccaactt--ctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
           ||| |  || |   ||   ||     ||||  ||| |      | ||  || ||| | || || |  | |  ||       || ||     ||||   | |||||| |||||||| |||||||||||||| || ||||| || ||||| ||||||||||| ||||| || |||||||  ||||| || || ||  | ||||||||
gtgtgtggtgatatcttcctctacctagtttttcagctttgctatcagggaattatttagctattg-gaatcaattgttttttatcatgtctaatattgtggctca---aatgcagGATTCTGGGACATGTATGACCCAGAGGGATACTCACTATGGTTCTGTGACTACAAGTACAACGATGAGAACATGGTGTCATTTGTCACGCTCAACAAGGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: AT1G57720.1 (Arabidopsis thaliana), 3'ss of exon 7
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaa-gttctgtgaa-ttgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
   ||      |  | || ||  ||| |             |      | || | | |  |||| | ||  | ||  |      | || |   | |||||||| |||||||| ||||||||||| || || ||||| || ||||| |||||||| || ||||| || |||||||  || ||||| || ||  | ||||||||
--ttagaggggtactcactatggtttatgggacatgtatggcccagagtctgaaagtacattctattaagctcaatgccttgaatgtttttcttcattgcagGATTCTGGGACATGTATGACCCGGAGGGGTACTCACTATGGTTCTGTGACTATAAGTACAACGATGAGAACATGGTCTCCTTTGTTACACTCAACAAGGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S33_218V6.1 (Physcomitrella patens), 3'ss of exon 6
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattga-actcaacatgtcttctcact---tattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
    | || |||  | |   |  | || ||    |       |||| |  ||| |       |  |   ||| | | | |   | |  |   |   | | ||||| |||||||| ||||  ||| | |||||||||||  ||||||| ||||| ||||| |||||||||||||||   ||  |||| ||||| ||||| || ||
--gca-ctttttagtcattctagtctg-cagagtcagagtgtttctctcatgtctcggacgtttggggctgatagtgagctaatttggtggttgtatgtggcagGATTCTGGGAAATGTTCGACGCTGAAGGTTACTCTTTGTGGTTCTGTGATTACAAGTACAATGACGAGAACCAAGTAACCTTTGTGACTATGAATAAAGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ14564 (Selaginella moellendorffii), 3'ss of exon 6
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
                                      ||| |  |||| |  ||  |   ||   || ||      |  |   | |  | |  ||||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||| ||||| || |||||||| ||| | |||||||| |||||||||||
-----------------------------------gtacaagtggtgtt-tccattgatcgcttgaaaatg---ctgattttgatcccaaatctttgcagGATTCTGGGAGATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

upper sequence: LOC_Os02g12794.3 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ26267 (Selaginella moellendorffii), 3'ss of exon 5
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
                                      ||| |  ||||     |||     ||  |||     |    || ||||| |     ||||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||| ||||| || |||||||| ||| | |||||||| |||||||||||
-----------------------------------gtacaagtggtgtttccattgatcgcttgaaaatgctgattctgatctcttccc-----ttgcagGATTCTGGGACATGTATGACCCCGAGGGATACTCCCTGTGGTTCTGCGACTACAAGTACAACGATGAGAACACGGTGCCTTTCGTGACGATGAACAAGGT

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|218505344|gb|FG953711.1|FG953711
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|29656571|gb|CB652846.1|CB652846
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|33795055|gb|CF323403.1|CF323403
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGNTGGTTTTGTGA
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagG-TTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTG-TGGTTTTGTGA
EST: gi|33679131|gb|CF307370.1|CF307370
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|29638694|gb|CB643703.1|CB643703
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|163918157|gb|EG715271.1|EG715271
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|218505075|gb|FG947175.1|FG947175
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|218484680|gb|FG966728.1|FG966728
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|29637990|gb|CB642999.1|CB642999
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|58597071|gb|CK007599.1|CK007599
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|218501329|gb|FG956585.1|FG956585
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGGTGGTTTTGTGAC
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTG-TGGTTTTGTGAC
EST: gi|218504332|gb|FG960754.1|FG960754
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|33664809|gb|CF295776.1|CF295776
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|218488618|gb|FG963896.1|FG963896
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|58663171|gb|CK051857.1|CK051857
EST:     ATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTAGGGATATGTATGACCCAGAAGGTTACTCCCTGTGTGTTTTGTGA
genomic: ATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCT-GGGATATGTATGACCCAGAAGGTTACTCCCTGTG-GTTTTGTGA
EST: gi|218490207|gb|FG966197.1|FG966197
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|29629868|gb|CB634877.1|CB634877
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|29637848|gb|CB642857.1|CB642857
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
EST: gi|58655937|gb|CK044617.1|CK044617
EST:     GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGG                         GTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT
genomic: GAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACT

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: 85

AACCCTCTTGATTTGCTCCCTCCAAGCAAGATGATCCTTGATGAGTGGAAGAGGTTATACTCAAACACAAAAACAAATTTCCGTGAGGTTGCTATCAAGGgtaagtttct ... cttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT
                                       ttctcac  putative branch site (score: 85)
                                     tcttctcacttatt  CT-rich tract
                     aattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatctctttgattaccattatttgtcatctgctcccaacttctgttgtgtatgaagttctgtgaattgaactcaacatgtcttctcacttattgcagGTTTCTGGGATATGTATGACCCAGAAGGTTACTCCCTGTGGTTTTGTGACTACAAATACAATGACGAGAACACTGTGTCCTTCGTGACCATGAACAAGGT

- - - - - - - - - - - - - - - - tgctccc
- - - - - - - - - - - - - - - - - - - - - - ctgttgt