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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os03g01910.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G041881_T01 (Zea mays), 3'ss of exon 2
aagatatactgggcttgtat-tttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgc-----atttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
     |     | ||| |   |||| |||  ||| | ||    | ||  |||      | ||  | |   |||  ||| | ||  || |      | |  || |||||||||||||||||| ||||||||  | ||||| ||||||||| ||||||| ||||| ||||||||| | ||||||||||  ||||||||||| || |||
----caccgaagccttttgcgtttgtgatatgatatgtt--ttattgagttgcttctggacccatagtcccatgctaacaatttatgagggaaaaaatgctgacagGAAGAAGAAGGCAGTCCACAAGACCGCAACCACCGATGACAAGCGGCTTCAGAGCACGTTGAAAAGAATTGGAGTGAACACTATTCCTGGTATTGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G110116_T01 (Zea mays), 3'ss of exon 2
aagatatactgggcttgt--attttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcat--ttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
 |   |  ||  || |||    |||| |||| | || |  |  |||  | | |  |  | | |     || |  | ||||   ||  |  ||   |  |||||||||||||||||||||||||||||| || ||||| ||||||||| ||||||| ||||||||||||||  | || | ||||| ||||||||||||||| |||
caagcac-ctaagcctgttgggtttgtgatctgttcatagagtcaacttctggacccatagtccc---atgctaactaatttatgagggacaaaatgctggcagGAAGAAGAAGGCAGTTCACAAGACCACGACCACCGATGACAAGCGGCTTCAGAGCACCTTGAAAAGGATCGGGGGGAACACCATTCCTGGTATCGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA01G18780.1 (Glycine max), 3'ss of exon 1
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtg-ctgtggcctttggattcatattaat-acttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
 |  |      || || |||  |    |    |  ||| |    |  ||||   |||| |  ||     |  |||| || | ||||| |   ||  |  |||||||||||| || || ||||||||||| || || |||||||| ||||||||||||||| |||| ||  ||||||||||    || ||||  || ||||| 
tatttgagtgaggtttctatgctatatttt--ttgtttgatatgtagattgcatctgttgagttaattattttattgatgatttgttttctgttgctcacagGAAGAAGAAAGCTGTCCACAAGACTACTACTACAGATGACAAAAGGCTTCAAAGCACCCTGAAGAGGATAGGAGTGAATGCTATCCCTGCAATTGAAGAA

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G12170.1 (Glycine max), 3'ss of exon 2
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatactt-gttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
    |  | |    | ||    |    |        |||||||    ||    |||| |  ||   | |  | |||||  || ||  |   ||      || ||||||||||| || |||||||| || ||||| |||||||| |||||||| |||||| |||| ||| |||| |||||   ||| || | ||| || |||
-gtttgcagtcaattcgttggctttattttttgtaattaaacacaaaatgaatctgttgtgttgaaagttctcttaatgttttgtcttatgttcggtctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCGGCTATTGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA12G04380.1 (Glycine max), 3'ss of exon 2
----aagatatactgggcttgta---ttttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
       || |  |||  || ||   |||| |||   || |    ||   || | ||||| ||    || |   || || ||     ||||  |   ||| |   || ||||||||||| || |||||||| || ||||| |||||||| |||||||| |||||| |||| ||| |||| |||||   ||| |||| ||| ||||||
tcactcaatttgttggctttttagtttttttggaattgaacacaaaatgcatctgttgtgttgaatgctctc--tttatgtt-----ttgtcttatgtttgttctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCTGCTATTGAAGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA11G12180.1 (Glycine max), 3'ss of exon 2
aagatatactgggcttgt--attttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatactt-gttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
    |  | |    | ||    ||| |  |   ||  || |||||    ||     ||| |  ||   | |  | |||||  || ||  |    |      || ||||||||||| || |||||||| || ||||| |||||||| |||||||| |||||| |||| ||| |||| |||||   ||| || | ||| || |||
--tttgcagtcaattcgttggctttagttttttataatt-aaacacaaaatgtatttgttgtgttgaaagttctcttaatgttttgtcttatgctcggtctagAAAGAAGAAGGCTGTCCACAAGACAACAACCACAGATGACAAAAGGCTTCAGAGCACCCTGAAGAGAATAGGGGTGAATGCCATCCCGGCTATTGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G73230.1 (Arabidopsis thaliana), 3'ss of exon 2
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaa-tacttgttgtg-catttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
                ||||  |    |  |   |||     ||| | |  |  ||     |||    | |||||   ||    || || |  | ||  ||| ||||||||||| ||||||||||| || || || |||||||||||||| || |||||  | || ||||| ||||| ||   |||||| |  || ||||| 
----------------gtatactcatttatgtcttttctgtgaatttgtgtttttgccatttttcatgttatattctctaaacattttgactctcatttcagAAAGAAGAAGGCTGTTCACAAGACCACTACAACCGATGACAAGAGGCTCCAGAGCACTCTTAAGAGAGTTGGAGTCAATTCCATTCCCGCCATTGAAGAA

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G17880.1 (Arabidopsis thaliana), 3'ss of exon 2
aagatatactgggcttgtattttgggatccgatcttttaa-acaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
      ||  | | ||   |      ||   ||  || || ||   | ||| | || ||   | ||   | ||   |  | | | | |  | ||   |||| ||||||||||| || |||||||| |  || ||||||||||||||||||||||||||  | || ||| | ||||| |||  |||||| | ||| ||||| 
-----gtatagagttttattcaaccaatttcattgttcaatacttagcatt-tactatgatttgtg---ttatgaaaccattcgatttttactt---gcagAAAGAAGAAGGCTGTGCACAAGACCAATACAACTGATGACAAGAGGCTTCAAAGCACTCTTAAGAGAATTGGAGTTAACTCCATTCCCGCTATTGAAGAA

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0053g00620.t01 (Vitis vinifera), 3'ss of exon 2
aagatatactgggcttgtattttgggatccgatcttttaaacaa--tgtattgtgctgtggcctttggattcat--attaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
    |    | |   |   | |||   |    |  |||| ||||  || |||   |||      |||| |  ||  |||| ||     | |   | |   |||| ||||||||||| |||||||| || ||||| ||||||||||| ||||||||||||||| | || ||| ||||||| ||   ||| |||| ||| || |||
----tgggtttgatattggtgttgatgtggtgtgatttatacaacttggattcccctgctatacttggttatatttattattatcaactttttttgtgctgcagAAAGAAGAAGGCTGTTCACAAAACAACCACAACTGATGACAAAAGGCTTCAAAGCACCCTAAAGAGAATAGGAGTCAATGCCATACCTGCTATTGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EDO98665 (Chlamydomonas reinhardtii), 3'ss of exon 1
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcat-attaatacttgttgtgcattt----atg-gcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
                           | ||     |  |     |    ||||  ||   |||||  |||    | || |  |  | |||| |    ||| |||||||||||||||| || |||||||| ||| ||||||| |||||| || | |||| |||| | ||  |  | || ||||||| ||| || || ||||| |||
--------------------------gtgcggcggctggaggcgcgctcggtgcactgctttttggggtcaccgctgatgcgcgcggggcatattgcaatgtgcagGAAGAAGAAGGCCGTGCACAAGACCACCTCCACTGACGACAAGCGGTTGCAAAACACCCTCAAGCGCCTGGGCGTGAACACCATCCCCGGCATCGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S28_196V6.1 (Physcomitrella patens), 3'ss of exon 2
-----aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
       | ||   ||  ||  | | |  || || |    |||    | | |  |||||  |      |  |  | | | |||     |||           |||||||||||| || ||||||||||| ||||||||||| ||||||||| | || |||||||||||  || | |||||||||| |||||| || || ||||||
ttcgtctgctactttgtactgctttgtgaggctctgggagtttccctagtctcatgtgccctatgtggtctacccttgtcaatttcaattggctg-----aacagGAAGAAGAAAGCTGTTCACAAGACCACCACCACTGACGACAAGAGGTTGCAGAGCACCTTGAAGCGACTCGGAGTGAACACCATTCCCGGAATTGAAGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S479_10V6.1 (Physcomitrella patens), 3'ss of exon 2
--aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgt-ggcctttggattcatattaatacttgttgtgcatt-tatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
  |||||||        ||| ||||  ||    |  | |  |    || ||  |    |    || |    |||||  | |  || ||  |     | |  |||||||||||| || || || ||||| ||| | ||||| ||||||||| | || |||||||||||| || | |||||||| | | ||||||| || || |||
taaagatatcacaaaactgttttttttga----aattctggatgtctgcataatctcattaatctattatatcataccattcattttttcgttccgtctaacagGAAGAAGAAAGCTGTGCATAAGACCACCTCAACTGACGACAAGAGGTTGCAGAGCACCTTGAAACGACTTGGAGTGAATACCGTTCCTGGAATTGAGGAG

upper sequence: LOC_Os03g01910.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ21066 (Selaginella moellendorffii), 3'ss of exon 1
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
                                          || |  ||| | |  |       ||||  |  | | | || | |       || ||||||||||||||||||| ||||||||  | ||||| || ||||||||| | |||| |||  | || ||| | || || |||| ||| || || || || |||
----------------------------------------gtaaagatttgggattagattggaagattt-tggtgagaattctggca-----atcgcagGAAGAAGAAGGCAGTGCACAAGACCGCGACCACCGACGACAAGAGGTTGCAAAACACGCTCAAGAGATTGGGCGTCAACACCATCCCCGGCATTGAGGAG

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|3769252|gb|AU033279.1|AU033279
EST:     AAGAAGATGGCGGGTGCCGTGCGCACCGGTGGCAAGGGCAGCATGCGCAG                         GAAGANGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCA
genomic: AAGAAGATGGCGGGTGCCGTGCGCACCGGTGGCAAGGGCAGCATGCGCAGgtatttttct ... tttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCA
EST: gi|218482454|gb|FG952463.1|FG952463
EST:     AAGAAGATGGCGGGTGCCGTGCGCACCGGTGGCAAGGGCAGCATGCGCAG                         GAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCA
genomic: AAGAAGATGGCGGGTGCCGTGCGCACCGGTGGCAAGGGCAGCATGCGCAGgtatttttct ... tttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCA

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: 39 (upstream exon), 57 (downstream exon)
Score: 106

ATGAATGTCGACAAGCTTAAGAAGATGGCGGGTGCCGTGCGCACCGGTGGCAAGGGCAGCATGCGCAGgtatttttct ... tttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG
                          tattaat  putative branch site (score: 106)
                     attcatattaatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatatactgggcttgtattttgggatccgatcttttaaacaatgtattgtgctgtggcctttggattcatattaatacttgttgtgcatttatggcagGAAGAAGAAGGCAGTTCACAAGACTACCACCACTGATGACAAGAGGCTTCAAAGCACCTTGAAAAGAGTAGGAGTGAACAACATTCCTGGTATCGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - gcttgta
- - - - - - - - - - - - - - - - - - -taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - gtgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgttg