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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

Basic information

species Oryza sativa
transcript LOC_Os11g43970.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G354532_T01 (Zea mays), 3'ss of exon 1
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
                             |   | |      || |  |  | |    |   | | | |||| |          ||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||
-----------------------------gtattatttcacctaatgggcaactgatgagattcactactgtctcaagGCTAACCAGTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 13
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
|||| ||   | | |        | | ||||| |  ||         ||||  ||||||  ||||    || ||  | ||||||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| || ||||||
gtattatttgacctagcgggca-actgatgagattcact--------tgtg--tctcaagcctaaccagtggttcgtttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 7
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
|||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  |||||||||||||||| ||||| ||||| |||||||| |||||||||||| |||||||||||||||| || || |||||||| |||||||||
gtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G170037_T01 (Zea mays), 3'ss of exon 4
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTC-ATTGATGAG---------------
|||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  |||||||||||||||| ||||| ||||| |||||||| ||| |||||||| |||||||||||||||| || || ||||||||  |||||||||               
gtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTATTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTTATTGATGAGGTATGCAAGCACACA

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G435582_T01 (Zea mays), 3'ss of exon 2
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
|||| ||  || | || |     | | ||||| |  ||    |||| |      ||||| |||||    || ||| |  |||||||||||||||| ||||| ||||| |||||||| | |||||||||| |||||||||||||||| || || |||||||| |||||||||
gtattatttcacctaa-tgggcaactgatgagattcac----tactgt------ctcaaggctaaccagtggtttgttaactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGTTGTTTTCTCACTAGCAAGTAAAATAGCACCCAGTGTTATATTTATTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 17
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
   |      ||   || ||    ||  ||  |||||     |  ||||      | | |   |||   || ||||  |  || ||||||||||| ||||||||||||||||| ||||| || || ||  | || || ||||| |||||||| ||||| ||  |||| |||
--gtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcagTGGTTTGGTGAAGGAGAGAAATATGTCAAAGCAGTCTTTTCTCTGGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 21
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctca-aagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
|||| |  |  |  || ||     ||  || ||||||     |  ||||      | | |||  ||||   ||||| | |  || ||||||||||| ||||||||||| ||||| |||||||| || ||  |||| || ||||| |||||||| ||||| ||  |||| |||
gtattaatgt-tgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttg-ttgcagTGGTTTGGTGAAGGAGAGAAGTATGTCAAAGCTGTCTTTTCTCTAGCCAGCAAAATTGCTCCAAGTGTTATTTTTGTTGACGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 18
-----gtatgatggcatccaaattttgcattaatgaggtgtacagtgtacta-tgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
      | ||      ||||| | |   ||| ||      |  | |    |  ||||  | ||||  |    |  ||    |  |   ||||||||||||| || || ||||||||||| ||||||||||||||  | || ||||||||  | || || ||||||||  ||||||||
gttaaatttgtccctctccaagtgt-atattgatctcacctttattagtttgctgtgcatatcaactcatgttcttgcccctctttgcttcagTGGTTTGGGGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA06G17940.1 (Glycine max), 3'ss of exon 22
gtatgatggcatcca--aattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttt-tctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
||  |||    | ||     |||   ||||||   | |    |    ||  || |  |   | ||  || || ||    | |   ||||||||||||| || || || ||||| || ||||||||||| ||  | ||||||||||| ||||| ||||| |||||  |||| || 
gttagatatgcttcactgggtttattttaatgtc-tctgttatcagttagttgttcattttaactgcattcttttcccattttgcttcagTGGTTTGGTGAGGGTGAAAAATACGTGAAAGCTGTTTTTTCCCTGGCAAGTAAAATTGCTCCTAGCGTGATATTTGTTGACGAA

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GLYMA17G13850.1 (Glycine max), 3'ss of exon 20
----gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
       |  |  |   | || | |  ||| ||      |  | |    |          |||  |    |  ||  | || |   ||||||||||||| || || ||||||||||| ||||||||||||||  | || ||||||||  | || || ||||||||  ||||||||
gttaaatttgtctctctctaagtgtatattgatttcacctttattagtttgctgtgcatacaactcattttcttgcctctttttgcttcagTGGTTTGGTGAGGGTGAGAAATATGTGAAAGCTGTTTTCTCTCTGGCGAGTAAAATTTCACCTAGTGTTATATTTGTTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 21
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgtttttt-ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
        | ||  |    ||  |    | |  ||   | | ||   |||  |  |  |   || |      ||     | | |  |||||||||| || |||||||| || || |||||||||||||| ||||||||||| |||||||||||||| || ||  ||||||||
--------gtattgatcacttaaaacggttacctg---actctatagtgttttctttgagattagacttgacttgagatttcgtgtagTGGTTTGGTGAGGGAGAGAAGTACGTTAAAGCTGTTTTCTCTTTAGCAAGTAAGATAGCTCCAAGCGTCATTTTTGTTGATGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 21
--gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
    ||    ||||| ||||  || | ||   || | |    || |     || ||   |||  |      |  |  |  | ||| ||||||||||| ||||||||||||||||| |||||||| |||||  |||| |||||||| || || || ||| | ||  |||| |||
gtaaatatgtgcatcaaaatggtg-actatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcagTGGTTTGGGGAAGGAGAGAAATATGTCAAAGCTGTGTTCTCTCTAGCTAGTAAAATTGCACCTAGTGTTGTTTTTGTTGACGAG

upper sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 22
lower sequence: PP1S27_195V6.1 (Physcomitrella patens), 3'ss of exon 17
--gtatgatggcatccaaattttgcatt--aatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgtt-----tt----ttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
   | || |    |  || ||||| | |  ||  | || | |||  |  ||       || |    |  ||||| ||     ||    |||||||| ||||||||||| ||||  ||||| ||||||||||| |||||  |||| ||||| || ||  | || ||||| || || |||||||||
gtttttgtttttttttaatttttggacttgaacaacgtttgcagaattttagtctcagcttattcatgcatgctattgatagttctaattctacttgcagTGGTTTGGAGAAGCTGAGAAGTATGTAAAAGCAGTTTTTACATTGGCAAGCAAGATTTCACCGAGCGTAATTTTTATTGATGAG

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|58684670|gb|CK073357.1|CK073357
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|58687870|gb|CK076557.1|CK076557
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|58692889|gb|CK081576.1|CK081576
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATCATGTCAAAAGCTGTTTTCTCATTAGCAA
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAAT-ATGT-AAAAGCTGTTTTCTCATTAGCAA
EST: gi|58607816|gb|CK035849.1|CK035849
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|163926070|gb|EG715026.1|EG715026
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|66922707|gb|CX109555.1|CX109555
EST:     AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: AAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
EST: gi|86831749|gb|CI301599.1|CI301599
EST:     CTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAG                         TGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT
genomic: CTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGT

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: 72 (upstream exon), 60 (downstream exon)
Score: 24

TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggc ... ctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG
                           agctaaa  putative branch site (score: 24)
                                    ctgttttttctacttt  putative PPT
                                       ttttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcagTGGTTTGGCGAAGGAGAGAAATATGTAAAAGCTGTTTTCTCATTAGCAAGTAAAATAGCTCCAAGCGTTATATTCATTGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG