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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA

Basic information

species Oryza sativa
transcript LOC_Os07g33954.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 2
aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctg--------ttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
       | |||      ||    |||   || | |||||   | |  |||| ||| || ||  |   |         | | | ||| ||| || ||   |   ||||||||||||||||| |||||||| ||||||||||||||  |||||| ||| ||||||||||||||||||||||||||||| ||||||||||||||||||||
------ttgtacttgtagcagtcgaaatcccaaactttgtcagtcactctga-acagcatattcagaagaagggtgactgaacctgtgttgttgtaa-cccaccgcagGATTCATGGGGGCAATGATCTCCAACCTGGCATTCGTCGTCCGGACCATCTTCTCCAAGAAGGGGATGAAGGGCAAGTCCGTGAGCGGGATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G11270.1 (Glycine max), 3'ss of exon 2
--------------------------------------aaagaaat-----atacaccagccac----gaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaa-attcgatg---cagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
                                       | || ||     ||||   || ||      | |   || | ||||| |   |       | | ||          |    ||  |  || |    || | | ||||   |||| || |||||||| ||||| || ||  |||||||||| ||||| || |||||||| ||||| ||||||||||| | ||| || || || |||||||||||
gtaagactatttgctgaaaaaaaaaaaaacaaggtttagatgagatttctcatactgtagacatttttaatacgatgtagaatttatcatttgtgtatatatatttttggtggttcaatattctaaatagagagaacacttgatgtttcagGCTTTATGGGGGCTATGATATCAAATTTGGCATTCGTCTTCCGCAATATATTCTCAAAGAAAGGGATGAAGGGAATGTCTGTTAGTGGAATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G27680.1 (Glycine max), 3'ss of exon 2
aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
    ||   ||    |   |  || |||      ||||  || |  |  ||  |  |||    | |||    |  | | |    |||  ||  | | |||| ||||||||||| ||||| || ||  ||||||| || ||||| || |||||||| ||||| ||||||||||| | ||| || || || |||||||||||
--gtaagactatttaaatgaaaaacaaggttgagattttctctt--atttggtagttcaa--tattctaaatagagagaacacttgatgat--gtttcagGCTTCATGGGGGCTATGATATCAAATTTGGCATTTGTCTTCCGCAATATATTCTCAAAGAAAGGGATGAAGGGAATGTCTGTTAGTGGAATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G03950.1 (Arabidopsis thaliana), 3'ss of exon 4
aaagaaatatacaccagccacgaaaaagtgcac-aatttgttcata-aacctgacacatcacatcaatctgttcat---cgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
       ||   | || |  |  |    | |   ||   | | ||  ||    |   |     |  |  |||| ||   || || || ||      |   | |||| || |||||||| ||||| |||||  |||| || ||||| || ||||||||||| |||||||| |||||||| ||||| ||||| | |||||| |||||
------gtacttaacaacatcctattgataccttaagaagctaatgcaattcaatgaaatgttttgagatgttgatatacgggtgtttcttgggggtt--ttcagGGTTTATGGGGGCAATGATATCGAATTTGGCGTTTGTGTTTCGTAACATATTCTCAAAGAAGGGAATGAAGGGGAAGTCAGTGAGTGTGATGAATTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 2
aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
   | || |  ||| | ||  ||| |   |    |  || | | |   ||   |  | |      | |||  | | |    ||  |||  ||   || ||| || |||||||| ||||| |||||  ||||||| ||||||||||| || || || ||||| |||||||| || ||||| |||||||| |||||||||||
---gtaaaactcacaatcctagaatattggtttcacatggtgacatttctttgat-ttatggtcttatgtgaaactt----tgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G54800.1 (Arabidopsis thaliana), 3'ss of exon 2
---aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattg-ctgaaaattcgatgc------------agGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
   | | | || | || |      |  | |       |  |||   |     ||| |  | | ||   | ||    |    | ||| ||  ||||  | |||            ||| |||||||| || ||||| |||||| |||| ||||||||||| ||||| ||||| |||||||| |||||||| ||||| ||||||||||||||||||||
gtaacatatatcttcatcttatttgttagatacattgaggtgtaattgggattgagatttgaaatggctttgcatgtttgattttggcttcaaatctgctgctccttacttttcagGTTTCATGGGAGCTATGATTTCGAACTTGGCTTTCGTGTTCCGTAACATCTTCTCGAAGAAGGGAATGAAGGGAAAGTCTGTGAGCGGGATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 2
----------------------aaagaaatatac-accagccacgaaaaagtgcacaatttgttc--ataaacctgacacatcacatcaatctgttca-tcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
                      |||||   | |      | | | |||   |    | |||| |   || | | ||| |  ||  ||   | | |  | |  || |||  ||    |  | |  ||| || |||||||| ||||| || || |||||||| |||||||||||||||||||| ||||  ||||||||||| ||||| ||  | || |||||||||||
gtgagaaggattgattaatattaaagattgaaattgatggtctcaaaattctcttgattttgatgtgatgatcatgatatttcttatgggtttttcaagttctgaatttgtgttgctatgttctagGGTTTATGGGGGCTATGATTTCAAATCTGGCATTTGTGTTCCGGAACATATTCTCAAAGAGAGGGATGAAGGGGAAGTCTGTTGGGGGAATGAACTACTA

upper sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S143_174V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------aaag----aaatatacaccagcca--cgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaa--aattcgat---gcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAG---GGCAAGTCGGTGAGCGGGATGAACTACTA
                                || |       | ||  |  |  |  |  ||| |    ||  | |||  |  |||  | |       |  ||  ||  |  ||| ||      |  | || | |   ||||||||  |||| || ||||| |||||| | || ||||| ||||| ||||| ||||| |||||||||||||     ||||||   ||  | || ||||||||   
gtattgtactgttagtattgcgtttgttcaacaaggtcgcgtgtttattctggataatctgaaagggatgcaggt-gtttttggacccaataag--gagttgatg-gtaaagggtgaatcatctgattactttggtatggcagGATTTGTGGGAGCCATGATTTCGAACGTTGCGTTCGTCTTCCGTAACATCTTCTCGAAGAAGGGGATGACAACCGGCAAGAGCGTTGGTGGCATGAACTA---

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|163928182|gb|EG713578.1|EG713578
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|58681314|gb|CK070001.1|CK070001
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|38479783|gb|CF963872.1|CF963872
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|58677764|gb|CK066451.1|CK066451
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|58687050|gb|CK075737.1|CK075737
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|58598525|gb|CK009053.1|CK009053
EST:     CGGCGGATGCGCCCTCGCCGCCATCAGCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|218501784|gb|FG956611.1|FG956611
EST:     TTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: TTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|58677768|gb|CK066455.1|CK066455
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
EST: gi|27554106|gb|CA998006.1|CA998006
EST:     CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTG                         GATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT
genomic: CGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATAT

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: 71 (upstream exon), 65 (downstream exon)
Score: 22

CTCGGCGAGCACTTCCCGGCGCCGGTCTACTTCTCCCTCCTCCCAATCATCGGCGGATGCGCCCTCGCCGCCATCACCGAGCTCAATTTCAACATGATTGgtgagtgagc ... ttcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA
 acctgac  putative branch site (score: 22)
                                       tgaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG