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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC

Basic information

species Oryza sativa
transcript LOC_Os05g05780.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 8
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttg--aagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
||    ||| | ||   |||  |  | | | ||||  | |     |   |  |  || ||   |||  | ||  ||  |||  ||||||||||| |||||||| ||| ||||||| || |||||||| || || ||| |||| || || |||||||| ||||||||||||||||||||| ||||||
gttg-ggatataattatcatgataactaattatagtactttaaaatgaactcttaataat---tgtttcttgcaacttttgcaaagGTTCTTCGCCCATTTCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGTCTACCTCCGAAGAAGGAAACCATACTTAAAGTTGGAATGTCTCAGATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 5
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
||    ||| |  | | | |  || | | |  |||  | |     |   |  | ||| ||| || |  |            ||||||||||| ||||| || ||| ||||||| || |||||||| || || ||  |||| ||||| || ||||| || |||||||||||||||||| ||||||
gttg-ggatatagttttcgtgatcaccaattttagtaccttaaaatgaactctttataatt-gtttctcgcaacttttgcaaagGTTCTTCGCCCATTCCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGCCTACCTCCAAAGAAAGAAACAATTCTTAAAGTTGGAATGTCTCAGATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
gtaacagatttgatatccatattctca--attgatagatc---atgttggttttccttgta-tgatttgtgtaacatgttacacttg--aagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
     | |||  | | || | || | |   |||  ||  |   |||||  | |  |   || |  |   | | |  |  ||    |   ||||| || || |||||||| ||||| ||| | || || |||||||||||||| || ||||| |||||||||||||| ||||| || || |||||  | ||||
---gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 8
gtaacagatttgatatccatattctcaatt--gatagatcatgttggttttccttgta-tgatttgtgtaacatgt-tacact-tgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
|||  ||  ||||      | |  |   ||  | |  |   || |    |    | || | || | |  ||  | | | ||   | ||||| || |||||||| || ||||| ||| | || || ||||||||||||||||| ||||| ||||||||||| || || ||||| || |||||  | ||||
gta--agccttgaagcttctttgattgtttagggtctactgtgataaaatgttatataataatgttttcaatttctgtgcatgattaagGTCCTCCGTCCATTCCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAAAAGGAAACCATTCTCAAAGTAGGCATGTCGCAAATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 8
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttga---agGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
||||    |      ||   ||| | ||  | |  ||  || |    |    | ||  | |  | | |  |  |     | |   |||| || |||||||| || ||||| ||| | || || ||||||||||||||||| ||||| ||||||||||| || || ||||| || |||||  | ||||
gtaagccttgaagcttcttcattgttaag-ggtctattgtgataaaatgttgtataataatgttttcattttctgtgtgtaattaagGTCCTCCGTCCATTCCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAAAAGGAAACCATTCTCAAAGTAGGCATGTCGCAAATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 8
gtaacagatttgatatccatattctca--attgatagatc---atgttggttttccttgta-tgatttgtgtaacatgttacacttg--aagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
     | |||  | | || | || | |   |||  ||  |   |||||  | |  |   || |  |   | | |  |  ||    |   ||||| || || |||||||| ||||| ||| | || || |||||||||||||| || |||||||||||||||||||| |||||||| || |||||  | ||||
---gtaaattacagaaccttcttttgattgttggaagtccttgatgttaatctggcacataattgtcattttcattttctatgtatatcaagGTCCTCCGACCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGATTGCCACCAAAAAAGGAAACTATTCTTAAAGTAGGCATGTCCCAAATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
        | || ||  |||||| |  ||  |  | | ||  |     | ||| |   | |  | || |   | |   ||| ||||||| || |||||||| ||||||||| | ||||| ||||| |||||||| ||||| ||||||||||| || ||||| |||||||| |||||| | ||||
-------gtatg-tactcatatttt--atcaa--ggttattctctaagttcttatgctaatcatttacc---tcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaacagatttgatatccatattctcaattga-tagatcatgttg-gttttccttgtatgatttgtg-taacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
|||   |||     | ||||    |  ||||| |  ||  ||||  || |   | ||| | |   || |  ||||| |   ||  |||||||||| |||||||| ||||| || || || || ||||||||||||||||| ||||| || ||||| || |||||||||||||| |||||| ||||||
gta-tggat---gcacccattccttgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgt-atctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 8
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
|||| |     ||  |||  ||| |  |    ||  | || |    |    |  |   ||   |     || |     ||  |||| || || || || || |||||||| || || || |||||||||||||| || || |||||||||||||| ||||||||||| || |||||| |  |||
gtaa-acccaagacctcctaattttttagctctaccttatttcatctcatttactgaaatggtttctgtatttctgttttttagGTCCTCCGGCCTTTCCTCCTTCGGAGACTGAAGTCAGATGTTGAGAAAGGCTTGCCTCCAAAAAAGGAAACAATACTTAAAGTAGGCATGTCTCAATTGC

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|58607651|gb|CK035684.1|CK035684
EST:     AAATCTCAGGGGAAAATGATCAACATGAAGTTGTTCAGCAGCTTCATAAG                         GTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGT
genomic: AAATCTCAGGGGAAAATGATCAACATGAAGTTGTTCAGCAGCTTCATAAGgtaacagatt ... acacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGT
EST: gi|29632571|gb|CB637580.1|CB637580
EST:     AATCTCAGGGGGAAAATGATCAACATGAAGTTGTTCAGCAGCTTCATAAG                         GTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGT
genomic: AATCTCA-GGGGAAAATGATCAACATGAAGTTGTTCAGCAGCTTCATAAGgtaacagatt ... acacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGT

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

CTTGTTGCCTGAAATATTTAGCTCTGCTGAGACTTTTGATGATTGGTTCCAAATCTCAGGGGAAAATGATCAACATGAAGTTGTTCAGCAGCTTCATAAGgtaacagatt ... acacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC
                                 gtgtaac  putative branch site (score: 32)
                         tatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagatttgatatccatattctcaattgatagatcatgttggttttccttgtatgatttgtgtaacatgttacacttgaagGTTCTTCGTCCATTTCTGCTTCGGAGGCTTAAATCTGATGTTGAGAAAGGTTTACCACCAAAAAAGGAAACTATACTTAAAGTTGGAATGTCTGAGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG