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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagctatcatttgcttcctttctcaatctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag

Basic information

species Oryza sativa
transcript LOC_Os05g10810.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G130749_T02 (Zea mays), 5'ss of exon 10
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagtttt-----caagctatcatttgcttcctttctcaat---ctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag
|||||  |||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||| |||||||||||||||||| || |  || ||     ||| |||  ||   |||| ||| ||||    | ||| |||  ||||||| ||   || |  || ||| || ||||||||  || | | ||||  |  || |||||||||||||    
GTTAAACATACTTGCTGAGATTCTTCGATTTGGTGACCGAGAATTCTACAAAGACTGGTGGAATGCAAAGACAATTGATGAGgtgaaatactaccgtgtttgttgcaacctagtata-acttcatttttcaactaacaaaaggaatctaggtaagcatagctgatgttgtgtatgttgtttgctgttgttgcttgtgttgctgtgcttggatgggatcag--

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA13G16560.1 (Glycine max), 5'ss of exon 10
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagct--atcatttgcttcct---ttctcaatctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag
||||| |||| | || ||| |||||||||||||||| |||||||||||| | |||||||||||||| |||||  ||||  || || |||  | | ||  | |   |   || ||| ||| |    || ||| |||  |  |||       |  |  | | || || ||| |     ||| | ||| ||  ||||| || ||   ||  |      ||||
GTTAAATATATTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACCAGGATTGGTGGAATGCCAAAACTGTTGA--AGATgtaagttatttgtcctgatattttgtcgtttacttacagtattttcagtcttcataaag-------agaaattgtgactttttgttt-----ttgtttctg-tatttgtgctgttgttgctgcttcca---tcag

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA17G06120.1 (Glycine max), 5'ss of exon 10
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagct--atcatttgcttcct---ttctcaatctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag
||||| ||| || || ||| |||||||||||||||| |||||||||||||| |||||||||||||| |||||  | ||  || || |||  | | ||  | |   |   |  ||| ||| |    || ||| |||   | ||      |      || ||   || | |   || ||||||  || | |   | |  ||                    
GTTAAATATCCTGGCAGAGCTTCTTCGATTTGGTGATCGTGAATTCTACAAGGATTGGTGGAATGCCAAAACTGTCGA--AGATgcaagttatttgtcctgatattttgttgtttacttacagtattttcagtctttcataaagagaatttgtgact-tattgttttcttgtatttttgctgttgttgctgcttccatcag------------------

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT2G19450.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagctatcatttgcttcctttctcaatctaaaagaagttaggtaaacagctctaacat-tctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag
|||||  ||| | || ||| ||||  | || || || ||||||||||||||||||||||||||||||||||   | |  || ||||    | ||  |  ||||   |  | ||      |||     | |    |   || ||| | |      | ||  |   |||  |   || || | ||  ||  |                         
GTTAAACATATTGGCAGAGCTTCTCTGCTTCGGGGATCGTGAATTCTACAAAGATTGGTGGAATGCAAAAAGTGTGGGAGATgtga---gctattttactcaaaagaaaacttatgatttttaatgttgtcgttgtttttgggtcatctaactaaccaaattcatgtattcactg-tcttcctttatcag-------------------------

upper sequence: LOC_Os05g10810.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv11s0016g01930.t01 (Vitis vinifera), 5'ss of exon 10
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagctatcatttgcttcctttctcaatctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag
||||| ||||||||||||| ||||||| ||||| |||||||| ||||| |||||||||||||||||||||||| |||| |||||           |||||  |  |    |    |   || || ||  |    |     ||  |  ||  |||||| |||||  |||   ||  |  || |   |||  |    | || |         ||||
GTTAAATATACTTGCTGAGCTTCTTCGTTTTGGGGACCGTGAGTTCTATAAAGATTGGTGGAATGCAAAAACAGTTGAGGAGgtag---------gttttttattttctgtgaagtgttttccttaagttg--tgtttcaagccatccatttctaac-ttctgcttgactattatttgtgtttgttgtatgcatttcctggttctacggatcag

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|29664361|gb|CB660636.1|CB660636
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29615462|gb|CB620474.1|CB620474
EST:     GTGACCGTGAATTCTACAAAGATGGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29664325|gb|CB660600.1|CB660600
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29641508|gb|CB646515.1|CB646515
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29646483|gb|CB651490.1|CB651490
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29664324|gb|CB660599.1|CB660599
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29664362|gb|CB660637.1|CB660637
EST:     ACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: ACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29646484|gb|CB651491.1|CB651491
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29614065|gb|CB619078.1|CB619078
EST:     GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAG                         TATTGGAGAAAATGGAATATG
genomic: GTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|66928227|gb|CX115075.1|CX115075
EST:     AAACAATTGATGAG                         TATTGGAGAAAA-GGAATATG
genomic: AAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG
EST: gi|29615460|gb|CB620472.1|CB620472
EST:     ACAAAGATTGGTGGAATGCAAAAACAATGGATGAG                         TATTGGAGAAAATGGAATATG
genomic: ACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG

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), 21 (downstream exon)
Score: 18

GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagaca ... gggatctcagTATTGGAGAAAATGGAATATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAAGTATACTTGCTGAGATTCTTCGATTTGGTGACCGTGAATTCTACAAAGATTGGTGGAATGCAAAAACAATTGATGAGgtgaaagacaatagttttcaagctatcatttgcttcctttctcaatctaaaagaagttaggtaaacagctctaacattctgtgtgatgtttgctcctgctacatgtgcggtcgtacttggatgggatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA