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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgccttgattacactgtcgctggagcctcgcattgtcatcgcctatcttctggagctaagaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG

Basic information

species Oryza sativa
transcript LOC_Os12g42876.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G149751_T06 (Zea mays), 3'ss of exon 10
gtaatttgccttgattacactgtcgctggagcctcgc-------------attgtcatcgcctatcttctggagctaagaa---atttctct---ttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG
|| |||  | |  | |   | |  |  |   ||| ||              ||  || |  |  |  | |||  ||   ||   |||||  |   ||| |||||||||||||||||||||||||| ||||||||||||||||||||||| |||||| |||||||||| || ||||||||||| |||||||| ||||||||||
gtcattctcttgaactgtgc-gctgtggagcccttgccagtgtgggagaggttcacaccaacatttctttggcactccaaactgatttccttctgttggcagATCCACACCCACATGTGCTACTCCAACTTCAACGACATCATCCACTCGATCATCGACATGGACGCGGACGTGATCACCATTGAGAACTCGCGGTCCGACG

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ05611 (Selaginella moellendorffii), 3'ss of exon 11
gtaatttgccttgattacactgtcgctggagcctcgcattgtcatcgcctatcttctggagctaa-gaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                     ||    |  ||  ||  ||   || || |      ||   ||   |   |||    |  ||||||||||||||| |||||||||||  |||||||||||||||||    |||||||| |||||||||| ||||||||||| ||||| ||||| || || || |
---------------------gtaaaagacgcgacgagtttctatagcttcgtgaatgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTCAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

upper sequence: LOC_Os12g42876.1 (Oryza sativa), 3'ss of exon 12
lower sequence: EFJ28889 (Selaginella moellendorffii), 3'ss of exon 11
gtaatttgccttgattacactgtcgctggagcctcgcattgtcatcgcctatcttctggagctaa-gaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                     ||    |  ||  ||  ||   || || |     |||   ||   |   |||    |  ||||||||||||||| |||||||||||  |||| ||||||||||||    |||||||| |||||||||| ||||||||||| ||||| ||||| || || || |
---------------------gtaaaagacgcgacgagtttctatagcttcgtgactgacactggcgttgtttgaaatccacagATCCACACCCATATGTGCTACTCCCACTTTAACGACATCATCACAGCCATCATCGACATGGACGCCGATGTGATCACGATCGAAAACTCTCGCTCGGATG

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|8404527|gb|AU091881.1|AU091881
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218488071|gb|FG946100.1|FG946100
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58695495|gb|CK084182.1|CK084182
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|84117659|gb|CD151426.1|CD151426
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATATGCTACTCTAACTTCAACGACATCATGCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58603308|gb|CK013836.1|CK013836
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|163927443|gb|EG713883.1|EG713883
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|163926579|gb|EG713595.1|EG713595
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218486915|gb|FG967742.1|FG967742
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACAACACCCAA                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29657694|gb|CB653969.1|CB653969
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|14574984|gb|AU197463.1|AU197463
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218496339|gb|FG945901.1|FG945901
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29619039|gb|CB624051.1|CB624051
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58601334|gb|CK011862.1|CK011862
EST:     CTGTTCACTCCTTCAGAATCACAAACTGCGGTGTTCAGGACACCACCCAG                         ATTCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|33676339|gb|CF304578.1|CF304578
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|33680371|gb|CF308610.1|CF308610
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|55408443|gb|CV720819.1|CV720819
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|396941259|gb|HO188468.1|HO188468
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29612828|gb|CB617841.1|CB617841
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|218478250|gb|FG951121.1|FG951121
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|109974700|gb|DT807056.1|DT807056
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58680570|gb|CK069257.1|CK069257
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|58662826|gb|CK051512.1|CK051512
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|33683114|gb|CF311353.1|CF311353
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|2428679|gb|C73142.1|C73142
EST:     TGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGGACACCACCCAG                         ATCCACACCCACATGTGGCTACTCTAACTTTCAACGACATTCATCCACTCC
genomic: TGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGG-ACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTG-CTACTCTAACTT-CAACGACAT-CATCCACTCC
EST: gi|29638193|gb|CB643202.1|CB643202
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAAGACACCACCCAG                         AATC-ACACCCACATGTGCTACTCTAACTTCA-CGACATCATCCACTCCAT
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagA-TCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCAT
EST: gi|29689518|gb|CB685793.1|CB685793
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
EST: gi|29622990|gb|CB628001.1|CB628001
EST:     CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAG                         ATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC
genomic: CTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATC

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: 75 (upstream exon), 75 (downstream exon)
Score: 323

AGAAGGTCTGCCACTCCGCAAGGCGGAGCATGCTTTCTACTTGGACTGGGCTGTTCACTCCTTCAGAATCACCAACTGCGGTGTTCAGGACACCACCCAGgtaatttgcc ... tctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcctcgcattgtcatcgcctatcttctggagctaagaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG
                                         tttctcttt  CT-rich tract
                                  taagaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttgccttgattacactgtcgctggagcctcgcattgtcatcgcctatcttctggagctaagaaatttctctttgacagATCCACACCCACATGTGCTACTCTAACTTCAACGACATCATCCACTCCATCATCAACATGGACGCTGATGTGATCACCATCGAGAACTCCCGGTCCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT