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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 20
gtacgttcttctgaaatgatctgaacatttt------tccatcattttctttgtattcat--gtgttattattagtt-ggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG---
||| |||||         |    ||  ||||      ||||  ||| |   |  | || |  |  |  | |  ||||  |  |  || | |||      || ||| || | |||  | ||     |||||| || ||||||||||| || ||  |||| || || || || |||||||||||||| |||||||||| ||| ||||||||   ||| |||| ||||| |||   
gtatgttctgtgctttacaggcaaatgttttcccagttccacaattcttaattgactctttagcctgctcaccagttcaggaaacaactttgacctgtgatgttgtatctttttgcttct----taacagTCCCTCCTGCATACTACGCACACTTGGCAGCATTCCGGGCTCGGTTCTACATGGAACCAGAGATGTTGGACAACCAGAC---GTCCAAGACCTCCAATGGCAC

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 20
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgt-attcatgtgtta------ttattagtt--ggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG---
||| || ||         |    ||| |||| ||| |       |||| ||  |    |||      | |   |||  |||  | | |||     |||| |  || || | ||  ||| |     |||||| || ||||||||||| || || ||||| || || || ||||||||||||||||| |||||||||||||||||||||||   |||||||||||||| |||   
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtga-tgctgtatcttttgcttctt-----aacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGAC---GTCGAAGAGCTCCAATGGCAC

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 20
gtacgttcttctgaa-atgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtcca---acagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG
           |||| |  |   | |||       |  | || ||||      ||||  |||| |   ||          |||  |  ||  |||| ||  |   |   | |  | ||    ||||||| || || || ||||| ||| |||| || ||||||||||||||||| |||||||||||  ||  | || |  |     | ||     |   | |   
-----------tgaacacaaaggggacaaagggaaacaaattacttta-----atgtactattctatatta---------tctatatttgtttcttacaacttagtggacttaattcatgtgcagTTCCTCCAGCGTATTATGCACATTTGGCAGCTTTTCGAGCGCGGTTCTATATGGAGCCAGACCTGCAGCAGGAGAATGGCTCCTCAGGTGGTGGCTCCAA

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 18
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG
                    | ||  || ||   |    |   |   |  |||| | | |||      ||    |  |||    |   ||||    | ||   |  |      ||   ||||||| || || || ||||||||| ||||||| || |||||||| ||||||||||| |||||    || || |      |     | |   |       ||
-------------------ccggagaatgttcaaaattctagatgctttgtcatttttaatttaagtgtgagttcacattacttactagaatacgacgttctctaatgatgaatc--gcagTTCCTCCGGCTTATTATGCGCATTTGGCTGCTTTCCGAGCGCGCTTCTACATGGATCCAGAAGCTTCCGATACTGGATCTCTAACTAGTGGGATGGGAGG

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 19
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGA--AGAGCTCCACTGG
                                                    |      ||   |  ||   ||     | |||     ||     ||   |  |  ||||  ||   |||| |||||||||||||| || || ||||||||||| || ||| | |||||||||||||| ||   ||| |||   | | |  |||| |   || | |  ||  
--------------------------------------------------gtaaagaccatagctc-tttcccataggctttgacaactaaagc-acaaagcaatcgtccttttctttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGG--CTGGCTCCGTCCACCGGAACACTGCTCC

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
lower sequence: EFJ14096 (Selaginella moellendorffii), 3'ss of exon 19
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGA--AGAGCTCCACTGG
                                            |      |||  | | ||     | ||    ||   || |||   ||    ||| |  | |||| ||       |||| |||||||||||||| || || ||||||||||| || ||| | |||||||||||||| ||   ||| |||   | | |  |||| |   || | |  ||  
-------------------------------------------gtaaagaccata-gctctttcccataggctttgacaactaaagcacaaa---gcaatcgtctttttct-----ttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGG--CTGGCTCCGTCCACCGGAACACTGCTCC

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|86492970|gb|CI135603.1|CI135603
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|163920974|gb|EG710111.1|EG710111
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|86435965|gb|CI107198.1|CI107198
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|87016539|gb|CI273749.1|CI273749
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCGGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|29636941|gb|CB641950.1|CB641950
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|88225229|gb|CI225145.1|CI225145
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|86594915|gb|CI258169.1|CI258169
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|29674861|gb|CB671136.1|CB671136
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|88906357|gb|CI375429.1|CI375429
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCATTTCGAGAACGGTTTTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|88969251|gb|CI382800.1|CI382800
EST:     ACACTTATGCACGGTGCACACGCTCTGTTTCTTTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: ACACTTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|8404400|gb|AU091754.1|AU091754
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|86431420|gb|CI085031.1|CI085031
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|86477748|gb|CI120381.1|CI120381
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|29636972|gb|CB641981.1|CB641981
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
EST: gi|27576993|gb|CA999687.1|CA999687
EST:     TTATGCACGGTGCACACGCTCTGTTTCTGTTG                         TTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA
genomic: TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACA

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: 32 (upstream exon), 71 (downstream exon)
Score: 7

TTATGCACGGTGCACACGCTCTGTTTCTGTTGgtacgttctt ... ggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG
                         tcttgcatttcttttt  CT-rich tract
                               atttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGAAGAGCTCCACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT