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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT

Basic information

species Oryza sativa
transcript LOC_Os10g20630.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA20G27000.1 (Glycine max), 3'ss of exon 11
------------------------------------------------------------------------------------------------------atgatcagacctttt-tcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAA-GAACACCATT
                                                                                                      |  || | |     | |||| |     |    |    |    | ||    |     |  ||   |  | |   |||   |   || || ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| |||||  ||||||| ||||| || ||   ||||||     | || ||| || |   |  
gtaagctttgtcacattttcagtttggtgatgctattagatatttagatgcctttttttattcaattctaaattttatatagcattgtggcatgcaacgagaagcattaaattcggtatcatctgagacttgttagaaactcaaatatgagaacatgaaatttgcaatttaccggtat---ttttgt-tggtgttt-ttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAGTTGTAAATCACGTGCACGAAGAAAGAGCGTGAA-

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G40340.1 (Glycine max), 3'ss of exon 11
----------------------------------------------------------------------------------------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAA-GAACACCATT
                                                                                                    ||||| | |  |  |    |  ||||   |  |    |  || || |     |||  | | || ||   ||    || |   || || ||||| || |||||||| ||||| ||||| |||||||| |||||||||||||| |||||  ||||||| ||||| ||  |   ||||||    |  || ||| || |   |  
gtaagctttatcacattctcagtttggtgatgctatttgatatttagatgccttattttattcaattctaaaattatatagcattgtggcatgcaatgaaatgattaaatttcgtatcatctgagacttgttagaaac-tcaaatatgagaacatgacgtttg-ccatttaccggtatttttgt-tggtgttt-ttgcagTCATATATGGATTCTGAAATCAGAGCCATCATGGCACAGTATATGCCCTTGGACAGCCAAGGAGAAATTGTAAATCACGTGAGCGAAGAAAGAGCGTAAA-

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G14740.1 (Arabidopsis thaliana), 3'ss of exon 11
-----------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctt---tatccatagcttatgacctgctaatattaatcccgtgtgctgtt--tctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                        |  |  |   | | |  | |  | | |  | ||         || |    ||||| |  |||  |      |  | | |    | | |||   |  | || |||  |||||||||||| ||||||||||| || |||||||||||||||||| ||||||| |||   ||| | || || ||    |||||||||     |    
gtaagcttttttaatctcttctgctcttttgttttctgttgtgttaatagcgaagattaatcttgtatttgccatatccgttacttggggaaaattgttttaacattcctatgcccctggttttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCATTGGACAGCCAACCCGAGATCCCGAACCACGTGAATGATGAACGCGCCTGAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G14720.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------------------------------------------------------------atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgttt--ctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                                                                                |  | | || || ||  ||  |  | | || ||   |     |  | |||| ||  |||  ||     |  ||| ||     | || |  |    || |||  |||||||||||| ||||||||||| || |||||||||||||||||||||||||| |||   ||||| || || || || |||||||||     | |  
gtaagctttttattcatccttctgctatttctgttagaagcaaaagattaatgttttatgttttggttgcctgagatgtctcttaaaacattgtt--ttatgtaacccgatatcgtc-ttggaattgtatcgattacttgggaaa-attgttatgaacttgctatgttcatggatttacagCAATACATGGACTCAGAGATCAGAGCCATAATGGCACAGTACATGCCACTGGACAGCCAACCTGAGGTCCCGAACCACACGAATGATGAACGTGCCTAAG

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv03s0091g00740.t01 (Vitis vinifera), 3'ss of exon 11
-atgatcagacctttttc-atttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGA-ACACCATT
 ||| |   |    ||   |  | |  ||   |  |   ||  |  | ||  |      ||| ||   |  | ||  | ||      || |   | |||||||||||||||||||| ||||||||||| || |||||||| |||||||| |||||||| |||  ||| || |||||||||     ||| ||  |  ||  |  
aatgttttaatgagttgagaaattgcaatgtaaggttgacaatatttgttggttttgcacttttggattattgat--tgatgtttcatggttgctttttcagTCATACATGGACTCGGAGATCAGAGCTATAATGGCACAATACATGCCCCTGGACAGCCAAACGGAAGTCCCAAATCATGTCTCTGAGGATCATGCATGAA-

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S227_69V6.1 (Physcomitrella patens), 3'ss of exon 13
atgatcagaccttttt-catttcgagatcagaaatgtccaccacatctttatccat---agcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
    |   |  | |   ||  | ||||||     | |  || |  || | |        | |||||    |      ||| | |  ||  |   | |    ||||||||||||||||| ||||| || ||||| ||||| |||||||||||||| |||||   | | || ||     | |||   |  || ||||   |     
----ttgcatgtctccacaaatggagatctctcttttgtactagttcgtaaagtgcttgaacttatttgattaacggatttagcttgtcggtgctgtggaacagTCATACATGGACTCGGAGATAAGGGCAATAATGGCGCAGTACATGCCACTCGACAGCTCAAGTGAAGTTAATCACCATCTGACCGAGGAAGCGTAAAGAC

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ30872 (Selaginella moellendorffii), 3'ss of exon 11
atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                             | ||| || |   | |  ||   | |     |  |     |||  ||     |  |     |||| |  |||| |||||||| || ||||| ||||| |||||||||||||||||||| || ||||| |||   || ||||   | ||     | || || |        |
-----------------------------gtaatatcaatt-cgtgattg--cttgatccagcaaaacttaacgttctctactggaaacttttcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGATGTGCATCACCACTTGCAAGAGGATGCTTGATTGT

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ31111 (Selaginella moellendorffii), 3'ss of exon 10
atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtg-ctgtttcttt-cagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                                  || |   |  ||| |  |  |   |     || | |  |||| | |  ||||| ||| |  ||  ||||| || ||||| || ||||| ||||| |||||||| ||||||||||| |||||||| ||    || || |     ||     | || ||||   |    |
----------------------------------gtacgtgatctctctggcattcatt-----ccggttggtattgagct-gtgtggctgctggttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCACCTCGAGGAGGAAGCGTAGTGAT

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ06539 (Selaginella moellendorffii), 3'ss of exon 10
atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtg-ctgtttcttt-cagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                                  || |   |  ||| |  |  |   |     || | |  |||| | |  ||||| ||| |  ||  ||||| || ||||| || ||||| ||||| |||||||| ||||||||||| |||||||| ||    || || |     |||    | || ||||   |    |
----------------------------------gtacgtgatctctctggcattcatt-----ccggttggtattgagct-gtgtggctgctggttggcagTCTTATATGGATTCGGAGATTAGAGCGATCATGGCGCAGTACATGCCTCTGGACAGCCAGAACGAAGTCCACCGCCATCTCGAGGAGGAAGCGTAGTGAT

upper sequence: LOC_Os10g20630.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ22768 (Selaginella moellendorffii), 3'ss of exon 11
atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                             | ||| || |      ||   |  ||     |  ||    |||  ||     |  |     |||| |  |||| |||||||| || ||||| ||||| |||||||||||||||||||| || ||||| |||   || ||||   | ||     | || || |        |
-----------------------------gtaatatcaattcgtgctcgcttgatccagcaaaac---ttaacgttctctactggaaacttttcctgtagTCTTACATGGATTCGGAGATTAGAGCTATCATGGCACAGTACATGCCGCTCGACAGCCAAAACGACGTGCATCACCACTTGCAAGAGGATGCTTGATTGT

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|58691626|gb|CK080313.1|CK080313
EST:     TGCTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|33692858|gb|CF321097.1|CF321097
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATAGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|58696080|gb|CK084767.1|CK084767
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|22307544|gb|BQ908766.1|BQ908766
EST:     AGTTGTGTGGCAGCAGGAAGTTATGGTTGTCTACAAATGACAGACTAAGG                         TCATACACTGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACT
genomic: AG-T-TGTGGCAGCAGGAAGTTAT-GTTGTCTACAAAT-ACAGACTAAGGgtaagctagc ... tttctttcagTCATACA-TGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACT
EST: gi|58660462|gb|CK049142.1|CK049142
EST:     TACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|218487201|gb|FG969113.1|FG969113
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|58688700|gb|CK077387.1|CK077387
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACCTATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|58654894|gb|CK043574.1|CK043574
EST:     AGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: AGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|33692859|gb|CF321098.1|CF321098
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATAGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
EST: gi|58677483|gb|CK066170.1|CK066170
EST:     TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGG                         TCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG
genomic: TGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTG

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), 58 (downstream exon)
Score: 27

TGTTCAGGGTAAAGCAGCTTGGGCTGCAGTTTGGGGAATCTTGATAGTCTTGGTAGTTGTGGCAGCAGGAAGTTATGTTGTCTACAAATACAGACTAAGGgtaagctagc ... tttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT
                           tattaat  putative branch site (score: 27)
                                          ctgtttctttc  putative PPT
                        taatattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatcagacctttttcatttcgagatcagaaatgtccaccacatctttatccatagcttatgacctgctaatattaatcccgtgtgctgtttctttcagTCATACATGGACTCTGAGATCAGAGCAATCATGGCACAGTACATGCCACTGGACAGTCAAGGGGAGGTGCCAAATCATACAAATGATGAAGAACACCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - -tttcatt
- - - - - - - - - - - - - - - - - - ccaccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgtgtgc