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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaa...

Basic information

species Oryza sativa
transcript LOC_Os01g02020.3
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02020.3 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM5G860137_T02 (Zea mays), 5'ss of exon 12
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatg--cagttatttgttgtactgattattcatgtatagttttgtgtaa-
||||||||||| |||||||||||  |||| |||||||||||||||||||| || || || ||||| ||||| ||| |||| ||||||||||  | || | | ||| || |||     |  | | |      |||||  ||||   ||||| | | |  |||||    | ||| |     |  ||   | 
ATTCTTAGACAGAAAAATGGAAAATTTGGTGTTGCTGGAGTTTGCAATGGCGGCGGCGGCGCTTCAGCCCTCGTTTTGGAGCTCATgtaagctcttcactttttttttgttcctcaaacttttttcccctgcaaaaggaaattttcagttctctatgatactgt---tccatctgatcgtcagtaggac

upper sequence: LOC_Os01g02020.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S160_44V6.2 (Physcomitrella patens), 5'ss of exon 12
--------------ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaa-------
               |||| |   | ||||||||  |  ||||||| ||||| || || ||||||||||| ||||| |||||  |||| ||||| ||||||||||     |    || |   | | ||    | |  |  |   ||    |    ||  || | |    | |  | |  || ||   || |||  |  ||       
TCACACTGCTCGGGGTTCTGAAGGAGAAAAATGGTCACTTTGGGGTCGCTGGTGTGTGTAATGGAGGTGGAGGTGCATCTGCTGTTGTGGTGGAGCTCATgtaaggtttgcatg-gtctaaccatttcccagattagcc-attcccttccactgttgtggtaact----gcaaaggt-gttgatacgtaatttcttacaatgttctc

upper sequence: LOC_Os01g02020.3 (Oryza sativa), 5'ss of exon 11
lower sequence: PP1S160_44V6.1 (Physcomitrella patens), 5'ss of exon 12
---------ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaa------------
          |||| |   | ||||||||  |  ||||||| ||||| || || ||||||||||| ||||| |||||  |||| ||||| ||||||||||     |    || |   | | ||    | |  |  |   ||    |    ||  || | |    | |  | |  || ||   || |||  |  ||            
CTGCTCGGGGTTCTGAAGGAGAAAAATGGTCACTTTGGGGTCGCTGGTGTGTGTAATGGAGGTGGAGGTGCATCTGCTGTTGTGGTGGAGCTCATGTAAGgtttgcatg-gtctaaccatttcccagattagcc-attcccttccactgttgtggtaact----gcaaaggt-gttgatacgtaatttcttacaatgttctcttcat

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|88449714|gb|CI539089.1|CI539089
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|86886429|gb|CI336132.1|CI336132
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACCTTCCTCCTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88470166|gb|CI407437.1|CI407437
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88261356|gb|CI364932.1|CI364932
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88457931|gb|CI542113.1|CI542113
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|89191076|gb|CI392929.1|CI392929
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|86600622|gb|CI356379.1|CI356379
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACCTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88276828|gb|CI395991.1|CI395991
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|22306530|gb|BQ907752.1|BQ907752
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|86868992|gb|CI334364.1|CI334364
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88272428|gb|CI386283.1|CI386283
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGACCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88322667|gb|CI542995.1|CI542995
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTNTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|89194176|gb|CI116613.1|CI116613
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|89190720|gb|CI392573.1|CI392573
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|86494598|gb|CI137231.1|CI137231
EST:     GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
genomic: GGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAA
EST: gi|88260275|gb|CI362568.1|CI362568
EST:     GAGGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCAT                         GCAACCATCACTATTTACACGTTCCTCGCTTGTGAAGTTGGCGCGAGCAAA
genomic: GA-GTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCG-TTGTGAAGTTGGCGCGAGCAAA

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: 58 (upstream exon), 54 (downstream exon)
Score: 22

ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccct ... cttgatgcagGCAACCATCACTATTTACACGTTCCTCGTTGTGAAGTTGGCGCGAGCAAAAATAGCACAAAGCTGAACTGTAAAGTACAGTAGCTCTATGTTTTCATCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTCTTAGACATAAAAATGGAAAGATTGGGGTTGCTGGAGTTTGCAATGGAGGTGGTGGTGCTTCTGCCCTTGTTGTGGAACTCATgtaagtccctcccatgtttgttcttctctggaaatgtctgagaaccaaaaaaaaatgcagttatttgttgtactgattattcatgtatagttttgtgtaa

- - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa