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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 3
ttagtgtatgatggatttgtttta---caagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
 |||| |     |  ||||||| |   |||| |          ||||   |||    ||||||| |  || |||  |    ||  ||  ||  |  |||| |||| || |||||||||||||| || |||||||||||||| ||||| ||||||||||||||||| |||||||| ||||||||||||||||||||||
atagtctgcttcgattttgtttcagagcaagaatcattgagcattttcactttcttatttgata-gcctgctcttctcattct--ctgattgctccaattcagGGGTATGTTGGCAACAAATCGGCCGTCTTTCCCCTGCAGCTCCTTGGCTTTGATGTGGATCCAATAAACTCTGTACAGTTTTCTAATCATACAG

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G398107_T01 (Zea mays), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgtt---ttagtttttcgctttgatatgta--tggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTT-CTAATCATACAG-------
| |||   |||  |  |||  || |  ||   |     ||      | || ||||| |  |  || |   | | |      | |||| |   |||| |  || |||| ||||||||||||||||| || ||||| |||||||| ||||| ||||||||||||||||| ||||||||  ||||||||| |||| |||||||       
tgagt---tgactgcgttgcctttcgtgtgacgggcggtgacgagcttgtgtttcgttcggggattttgttagcccaaatagtctgcatggattttgt--ttcagGGGTACGTTGGCAACAAATCGGCCGTCTTCCCCCTGCAGCTCCTCGGCTTTGATGTGGATCCAATAAACTC--TACAGTTTTTCTAACCATACAGTGATACA

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 2
---ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggt-ctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
   |   | |||| | || || |   ||   |  |   || ||| |  || | | | |   | |  | || | |  ||     || || ||  |||    ||||||||| ||||| ||||||||||| |||||||| || ||| |  |||| | |||||||||||| || ||||| ||||| || || ||||||||||
ctgtctctctatgcttgagttctgcaacttttttttttttgtgtgtgtgtgtgt-gttaccagaaatgtgatgccattttatatgtctattactttc---ttagGGATATGTTGGTAACAAATCAGCTGTCTTTCCTCTTCAATTGTTGGGGTATGATGTGGATCCAATCAACTCTGTACAATTCTCGAATCATACAG

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 2
-----ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
       | |  |  ||    || | |    |||      | |||| || ||  |  | ||  || ||| |  |   ||         ||| | |||    ||||||||| |||||||| ||||| || ||||||||||| || || ||||||| |||||| ||||| || || || |||||||| || ||||| ||||
aaacaccatttcaacataagcttatgt----agttacatttaatgtgtttgtggta-gattatatttgtgtcttaacttcattaccattttctatttccccttagGGATATGTTGGCAATAAATCGGCTGTCTTTCCCCTCCAGCTACTGGGCTATGATGTCGATCCAATCAATTCAGTACAGTTCTCAAATCACACAG

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ27991 (Selaginella moellendorffii), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
                                   | |    | | | | || ||    |     || ||    | || |   |  | |  |  |   ||||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| |||||                       
----------------------------------gtaagcgctcaatatctcactggattgcaagtgatc--ccgagctt--ttactctactcgagacagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------

upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29421 (Selaginella moellendorffii), 3'ss of exon 1
ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
                                   | |    | |   | || ||    |     || ||    | || |   |  | |  |  |   ||||||||||||| || ||||| || ||||||||| |||| |||||||| || ||||| |||||||| |||||                       
----------------------------------gtaagcgctcaaaatctcactggattgcaagtgatc--ccgagctt--ttactctactcgagacagGGATACGTTGGAAATAAATCGGCGGTCTTTCCCTTGCAGCTCCTGGGATTCGATGTTGATCCGATCAACTCC----------------------

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|88580749|gb|CI697698.1|CI697698
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88339276|gb|CI633847.1|CI633847
EST:     TTCCCTCCGACACGGGANGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88355870|gb|CI625499.1|CI625499
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGAAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88341926|gb|CI644263.1|CI644263
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACCCCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88337186|gb|CI628272.1|CI628272
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|58661072|gb|CK049752.1|CK049752
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         TGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCGTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88385774|gb|CI566636.1|CI566636
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|88424098|gb|CI689800.1|CI689800
EST:     TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: TTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     GCGTGCTCAGCATCCAGTCCCACACCGTCCAG                         GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT
genomic: GCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTT

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: 43 (upstream exon), 73 (downstream exon)
Score: 7

GCGGCGGCGGAGGACGGCGATGGCGCGGCCGCCGGTGCTCTCCGTCGCGCTTCCCTCCGACACGGGACGCGTGCTCAGCATCCAGTCCCACACCGTCCAGgttccttctt ... tttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG
                                            ttttaat  putative branch site (score: 7)
                                cctgcctttttttttt  CT-rich tract
                                      ttttttttttaattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtgtatgatggatttgttttacaagtagtgaattatgttttagtttttcgctttgatatgtatggtctgttgggcctgccttttttttttaatttagGGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG

- -gtgtatg
- - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgg