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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT

Basic information

species Oryza sativa
transcript LOC_Os11g26910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G101446_T01 (Zea mays), 3'ss of exon 1
tgaactatgtattccttttgtggctgaatgttgatc-tgtgctttagccatagtgattactgcttcttataccatgttt-atttgattctca---aatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
   ||  ||| ||  |||  |   || ||  | ||  | | || ||   || || |||| || ||     ||    | | ||| | |||||    |||   | |||| || ||||| || |||||||||||  |||| ||||| || || |||||||||||||||||||||||||| ||||| || || ||||| ||||||||||
--cacactgtttttgtttgatttttgtatcgtaattatatactgtaa--attgtaattattg-tttgagcactgcttctgattcgtttctcccctaattttatagGCTGCAAACTATCTGAACATCAAGGGTCTGCTCGACCTGACCTGTCAGACTGTTGCTGACATGATCAAGGGCAAGACACCAGAAGAGATTCGCAAGACCT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G08440.1 (Glycine max), 3'ss of exon 1
tgaactatgtattccttttgtggctgaatgt----tgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
  |  | ||||||  || ||      ||||     | | || || ||||   |    | | | |   |  ||   ||| || || |||   |    |     |||| || |||||| | ||||||||| |  ||||||||||||| || || ||||| || ||||||||||||||||||||||| ||||| || ||||||||||
--atgtttgtattgtttgtgcattgcaatgccacataaactctg-tttatttagtaggttaagtctgtactaatacatattaatgtgacaattttctttt-tagGCTGCTAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGTCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCAGAGGAAATTCGCAAGACCT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G05120.1 (Glycine max), 3'ss of exon 1
--tgaactatgtattccttttgtggctgaatgtt-gatctgtgctttagccatagtgattactgcttcttataccatgttt-atttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
       | || | |  || | ||  | ||| |  | | |   |||||   ||    ||||   ||     | |  ||||| ||   | | |   ||||   |||| || || ||| | || |||||| |  |  ||||||||||||||||||| || || |||||||||||||| |||||||||||||| || |||||||| |
gcctgtgtgtgcaatatttgtatgttttaatatcaggtttactcttta-ttatgtcaattaacactggcattcctttgttttatgaaaattttctatcc---agGCTGCAAATTACTTGAATATCAAGAGCCTTTTGGACCTTACTTGCCAGACAGTAGCAGACATGATCAAGGGAAAGACTCCTGAGGAAATTCGCAAGACAT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G23230.1 (Glycine max), 3'ss of exon 1
tgaactatgtattccttt-tgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatccc----acagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
| | |  ||||  | ||| | || |||  ||||    | |  ||||  | ||| | |||||  || ||||  ||  || |     ||   ||||  |    |||||| || |||||| | ||||||||| |  |  ||||||||||||||||||| || || |||||||||||||| |||||||||||||| || |||||||| |
taaccattgtagacttttgtctgcctg--tgtttgcatat-ttttaatcttag-gtttactctttattatgtca-attaacactctttcaaaatttcctatacagGCTGCAAACTACTTGAACATCAAGAGCCTTTTGGACCTTACTTGCCAGACAGTAGCAGACATGATCAAGGGAAAGACTCCTGAGGAAATTCGCAAGACAT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA01G36850.2 (Glycine max), 3'ss of exon 1
tgaactatgtattccttttgtggctgaatgttg-atctgtgct-ttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
  |    || |||   |  |     |||||    || |   || |||   |    | | | |   |  ||   |||||| || |||   |     |    |||| ||||||||| | ||||||||| |  ||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| || ||||||||||
-catggttggattatctgggcaatggaatgccacatatactctgttaattagtaggttaaatctgtactaatgcatgttaatgtgacaatttt-ccttttagGCTGCGAACTACTTGAACATCAAGAGCCTGCTGGACCTTACATGCCAAACTGTAGCCGACATGATCAAGGGGAAGACTCCCGAGGAAATTCGCAAGACCT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0038g02480.t01 (Vitis vinifera), 3'ss of exon 3
-tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttat---ttgattctcaaatccc-acagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
 || | | |  |    || | |  |  | | || |      || |    ||  ||||   |     |   | ||||| |||   |  ||||||   | |   ||||| || ||||| ||  | |||||| |  || ||||  | || ||||| || |||||||||||||||||||| ||||||||   ||| || |||||||| |
ttggattcttgag---ttgtatatcctactcttaaa--actctctgtttatgatgatgggtttgggtccaaacatgtgtatcaatcaattctctggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGTCGGAAATTCGCAAGACAT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0038g02500.t01 (Vitis vinifera), 3'ss of exon 1
-tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
 |   ||||    |  ||| |||  |     | || || |   ||   | | ||| ||   |  | | |  | ||  |    |  ||| |   ||   ||||| || ||||| ||  | |||||| |  || ||||  | || ||||| || |||||||||||||||||||| |||||||| ||||| || |||||||| |
atatcctattcgctaatttggtgattttccctagaactttttcttgtgccttgtgtttctcgtgtatcaatcaatcctccggttcttc-cggttcttgcagGCAGCAAACTATCTAGATATCAAGAGCCTGTTGGATTTGACCTGCCAAACAGTTGCTGACATGATCAAGGGAAAGACTCCGGAGGAAATTCGCAAGACAT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0038g02490.t01 (Vitis vinifera), 3'ss of exon 3
tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccata----gtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
  | || || ||  | | | ||      || |||| |   |   | |  |     |||  |  || ||||| |    | |  ||    |  ||   ||   ||||| ||  | || ||  | |||||| |  ||  |||  | || ||||| ||||||||||||||||| ||||| |||||| | ||||| || ||||||||  
-aagctttgaatatcctatttgctaatttggtgattttcccaagaactttttcttgtgccttgtgtttcttgtg---tatcaatcaattcttcggttcttgcagGCAGCAGATTATCTAGATATCAAGAGCCTGTCGGATTTGACCTGCCAAACTGTTGCTGACATGATGAAGGGAAAGACTGCGGAGGAAATTCGCAAGACAC

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv18s0001g14860.t01 (Vitis vinifera), 3'ss of exon 2
-------tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
        |||| || | |   | |  |  ||  || ||||| |   |  |||  | |   |||     |  ||  ||    ||| | ||  | | |       ||||| || ||||| || ||||||||| |  | ||||| |||||||| |||||||| ||||||||||| ||||| |||||||| |||||||| ||||| || |
gtcatggcgaacaat-tttagatatcatatct--attttgatatac-cagtagaaagaaaaatttacagtggtttgacataatttgtgtgtatttga---ttttcagGCAGCAAACTATCTGAACATCAAGAGTCTCCTGGATCTTACTTGTCAGACTGTGGCTGACATGATAAAGGGCAAGACTCCAGAGGAGATTCGCAAAACTT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP05410 (Chlamydomonas reinhardtii), 3'ss of exon 1
------------------------------tgaactatgtattccttttgtggctgaatgttgatctgtgct--ttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
                              |   ||  | ||  |  ||   || |       ||| |   |   ||  ||| | ||      | ||| |  |    |  ||  |  |||||     ||||||| ||||||||||| |||||||||||  |||||||||| || ||||||||||| ||| | ||||| |||||||| || || ||||||||||||||||| |
gtaagcgcgcgagaaatttggagcacctcgttcgct-cgcatggcccttagagccgcgcccccatcggccatggctatgcattgcgagcgagacgtctaacgc-gcatgcatgcggctctcacgcaacacagGCTGCGAACTACCTGAACATCAAGGGTCTGCTGGACCTGACCTGCCAGACTGTGGCTCAGATGATTAAGGGGAAAACGCCAGAGGAGATCCGCAAGACGT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S9_292V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
                                                                                  ||     || |    || || |||   |         |||  || |     ||||  | |  | || |   |  | |  |   ||  |   |    |||||| ||||||||| | |||||||||    |||||||| | || |||||||| || || |||||||| ||||||||||| || ||||||||| | || || |
gtaagtgatgtgcatgcgaccctgtttgttgcgtgcagggcgggggatggggtgcatcccagcgggggcggaagcgcgatgatggcgcgtgcaacgtttgtggggcgagagaggagggggtgacttgg----ggtgaggagttgtgctgacgtcggggtggtg-aatgatggga----acagGCAGCGAACTACTTGAACATCAAGAACCTGCTGGACTTGACGTGCCAGACGGTGGCGGACATGATAAAGGGGAAGACGCCGGAGGAGATCAGGAAAACGT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S7_342V6.1 (Physcomitrella patens), 3'ss of exon 2
--tgaactatgt-attccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatccca-cagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
  |  |  | || ||  || |  |  || ||||       | ||||| |   | || ||   |||| | || |  | | ||| | | |||| |  |   | ||||| || || ||| | |||||||||   ||| | || || ||||||||||| || || |||||||||||||| ||||| |||||||||||||| ||||| |
tttagagcacgtcatggctgtcttttcttaatgcc--ctagcgcttttgaatttgt-atccttgctacctaaatgaggcttaat-gtttcttatttgtgaacagGCGGCCAATTACTTGAACATCAAGAATTTGTTAGATCTGACTTGCCAGACCGTAGCGGACATGATCAAGGGTAAGACCCCTGAGGAGATCCGTAAGACAT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ22022 (Selaginella moellendorffii), 3'ss of exon 1
------------tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttat--accatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
             |  | || | ||||     |        | |  |||  | ||| |   | | | || |  ||    ||  |    | | || || || |    |    |||||||||||||| |||||||||  |   |||||||| || || ||||| || || || |||||||||||||| ||||| || ||||||||||||||||| |
gtaggatttcttcgttcgatttcttcccccctttttctctcgcttttct-cgttttgggtcttgagctttcgactgacaatcgatttgggtgatctggttttgcgttgttccagGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

upper sequence: LOC_Os11g26910.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ18284 (Selaginella moellendorffii), 3'ss of exon 1
---tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccat--gtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
    ||  | |   |||  ||| |  |    | ||  |||  |||||   | |  ||  |  ||    ||  ||      |  |||||  |      | ||  ||||||||||||| |||||||||  |   |||||||| || || ||||| || || || |||||||||||||| ||||| || ||||||||||||||||| |
gtaggatttcttcgttcgatttcttcccccctttttctct-cgcttttctcgttttgggtcttgagctttcgactgacaatcgatttgggtgatttgttcc--agGCCGCGAACTATCTCAACATCCGGAACTTGCTGGATCTGACGTGCCAAACCGTGGCGGACATGATCAAGGGCAAGACCCCGGAGGAGATCCGCAAGACTT

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|30229010|gb|CB966901.1|CB966901
EST:     ACGCCGACTTCGTCAAGGTCGACCAGGCCACCCTCTTCGACCTCATCCTG                         GCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACT
genomic: ACGCCGACTTCGTCAAGGTCGACCAGGCCACCCTCTTCGACCTCATCCTGgtataaaagc ... aatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACT
EST: gi|33685164|gb|CF313403.1|CF313403
EST:     ACGCCGACTTCGTCAAGGTCGACCAGGCCACCCTCTTCGACCTCATCCTG                         GCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACT
genomic: ACGCCGACTTCGTCAAGGTCGACCAGGCCACCCTCTTCGACCTCATCCTGgtataaaagc ... aatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACT

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: 149

CGCCGCCGCAGCCGTGCCGCCGCCCTCCGGCGAGGACCTCAAGAACTGGGACGCCGACTTCGTCAAGGTCGACCAGGCCACCCTCTTCGACCTCATCCTGgtataaaagc ... aatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT
                                 atttgat  putative branch site (score: 149)
                           atgtttatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaactatgtattccttttgtggctgaatgttgatctgtgctttagccatagtgattactgcttcttataccatgtttatttgattctcaaatcccacagGCCGCGAACTACCTCAACATCAAGGGGTTGCTGGACCTTACTTGCCAGACTGTTGCTGACATGATCAAGGGGAAGACTCCTGAGGAGATCCGCAAGACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - -tatgtat
- - - - - - - - - -gtggctg
- - - - - - - - - - - - - -atgttga
- - - - - - - - - - - - - - - - - - -gtgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattct