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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccatccatccatccatccaactagctagtagtagctactgctgctatcctggagtgatcatgaactggttcttgtcttcttgatcatgacatgaacgaactcaactcatcgtgccatatgaattgtgtttgtttgcattcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g66850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G329002_T01 (Zea mays), 3'ss of exon 1
gtatccatccatccatccatccaactagctagtagtagctactgctgctatcctgg-agtgatcatgaactggttcttgtcttcttgatcatgacatgaacgaactcaactcatcgtgccatatgaattgtgtttgtttgcattcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG
                                           | |  |||   |  | | |||  |    | |||||   ||| |   ||| |  |||  |   || | | |      ||||||   | | | ||  ||||    |||||||||||||||||| |||||||||||||||||| ||||||||||||||||||| |||   ||||||||| |  || ||||||||
-------------------------------------------gttcatatggagctatttatctagcgtcgcttctttgtttcctt-ccattatttgatgg---tctatttacacacacatatg---tatatatgcatgcac---tgcagTGTGCTTGGATGGAAGCCCGCCGGGCTACCACTTGCAGAGAGGCTTCGGCTCCGGATCCCACAGCTGGATCGTCTATCTTCAG

upper sequence: LOC_Os01g66850.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G349428_T01 (Zea mays), 3'ss of exon 1
gtatccatccatccatccatccaactagctagtagtagctact-gctgctatcctggagtg-atcatgaactggttcttgtcttcttgatcatgacatgaacgaactcaactcatcgtgccatatgaattgtgtttgtttgc---attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG
                                  |||   ||| ||| || |||| | ||  ||  ||  || |     |||||  || ||          |   |||  ||||| |||     |   |  || |   ||||   ||  ||  ||| ||||||||||| ||||||||||  ||||| || | ||||||||||||||| |||   | ||||||| |  || ||||| ||
----------------------------------gtattcactcgcttctttccttgcgttcattttgcgctagc----gtctttgtgttccccgggctgcctcgctc--ctcattgtgtatggttgctcttgctccgttgctcgatcgttatagTCTGCTTGGATGGCAGCCCGCCGGCGTACCAGCTCCGGAGAGGCTTCGGCTCCGGATCACGCAGCTGGCTCGTCAATCTTGAG
















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|33671653|gb|CF299892.1|CF299892
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88340205|gb|CI652554.1|CI652554
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|33664175|gb|CF295142.1|CF295142
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGATTTTTGCGCCG                         TGTGCTTGGATGGGATCCCGCCGGGCTACCACCTGCTTAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88721594|gb|CI744893.1|CI744893
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88720015|gb|CI745314.1|CI745314
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88695161|gb|CI739199.1|CI739199
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|13420831|gb|AU174921.1|AU174921
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|87023793|gb|CI288146.1|CI288146
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88731754|gb|CI753474.1|CI753474
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88417949|gb|CI596626.1|CI596626
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCAACTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88579191|gb|CI688168.1|CI688168
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAAGCC-GCCGGGCTACCACCTGCAGAGAGGCTTCGGC
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGA-GCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGC
EST: gi|88417964|gb|CI596641.1|CI596641
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88368321|gb|CI577592.1|CI577592
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|163921121|gb|EG710147.1|EG710147
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88417991|gb|CI596668.1|CI596668
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|66914214|gb|CX101062.1|CX101062
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
EST: gi|88342448|gb|CI645970.1|CI645970
EST:     GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCG                         TGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT
genomic: GGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCT

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), 73 (downstream exon)
Score: 22

CCCTTCCGGCTTCTCCTCCTGCTCCTGGCCGCCGCCGTCGCCCGCTCGGTGGACGGCGTCGAGCTGACCCTCCTCACCGGCGCTCGAGAGAAGGGCGCCGgtatccatcc ... attcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaacgaactcaactcatcgtgccatatgaattgtgtttgtttgcattcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG
                                            cattctt  CT-rich tract
                        atatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccatccatccatccatccaactagctagtagtagctactgctgctatcctggagtgatcatgaactggttcttgtcttcttgatcatgacatgaacgaactcaactcatcgtgccatatgaattgtgtttgtttgcattcttgcagTGTGCTTGGATGGGAGCCCGCCGGGCTACCACCTGCAGAGAGGCTTCGGCTCTGGAGAGCACAGCTGGTTTATCCATCTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG