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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCGGCTCCGTGGTCAACGAAGCCAGCCTTGGGAGCTTCATGGGTTACATGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtccttgttgcctgccctttttccagttctgatccttctctccctgtttgactcaactttgtggatgtctagatgagcaatccaatcacttgaca...

Basic information

species Oryza sativa
transcript LOC_Os12g05680.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g05680.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G366264_T01 (Zea mays), 5'ss of exon 6
---TGGCGGCTCCGTGGTCAACGAAGCCAGCCTTGGGAGCTTCATGGGTTACATGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtccttgttgcctgccctttttccagttctgatccttctctccctgtttgactcaactttgtggatgtctagatgagcaatccaatcacttgaca---
      ||| ||  || || ||||  ||||| |   ||||||||||||| | |||||||||||||| ||||||||||||| ||||||||  ||||| |||||||| | |   |     |    |||  |||  |  |  ||  |        |   |    |  |  |     | | |||||||||||   || ||| ||| |   
GGCCAACGGATCGCTGATCGACGACACCAGCAT---GAGCTTCATGGGTCAAATGGCCCTTGCCCTTGGCAAGCTGTCCAGCCTTGAAGTTTTTGTGATACAGgttacggtttcacatcaaatcctcattcttgacc--attatgacagtgttacatagtcctccactcaaactttgtagatgagcaagt-aaccacctgatagga

upper sequence: LOC_Os12g05680.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G030877_T01 (Zea mays), 5'ss of exon 11
---TGGCGGCTCCGTGGTCAACGAAGCCAGCCTTGGGAGCTTCATGGGTTACATGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtga--agtccttgttgcctgccctttttccagttctgatccttctctccctgtttgactca-actttgtggat-gtctagatgagcaatccaatcacttgaca
    || || ||  ||    |||| |||| | |   |||||||||| |  | ||||| |||||||| ||||| ||| ||||||||||||||||||| |||||||| |   || ||       |      | || | |    ||  | || |  | || | |     |||  || ||| |     |    | |||    | |      
GGCCGGTGGGTCTCTGACTGACGACGCCAACAT---GAGCTTCATGAGCCAAATGGCTCTTGCCCTCGGCAAACTGGCCAACCTTGAAGGCTTTGTGATACAGgttatgggttctcaccaaatctagaatctcaaatcaatatgttactatgacagtgtcataggtactccgtagatagatcctacacacgatctgggctccc----
















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|86496759|gb|CI139392.1|CI139392
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87040460|gb|CI195082.1|CI195082
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87041632|gb|CI196254.1|CI196254
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|88968885|gb|CI098962.1|CI098962
EST:     CAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: CAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|88956467|gb|CI092718.1|CI092718
EST:     AAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: AAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|88228663|gb|CI228143.1|CI228143
EST:     ACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: ACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87041136|gb|CI195758.1|CI195758
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|29641186|gb|CB646193.1|CB646193
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87041108|gb|CI195730.1|CI195730
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87040970|gb|CI195592.1|CI195592
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
EST: gi|87040449|gb|CI195071.1|CI195071
EST:     TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAG                         GCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA
genomic: TGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACA

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: 36 (upstream exon), 74 (downstream exon)
Score: 2

TGGCGGCTCCGTGGTCAACGAAGCCAGCCTTGGGAGCTTCATGGGTTACATGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtcct ... ggatttccagGCTGATAACTTGAGGCAACAGACTCTTCATCAGATGCACAGAATTCTGACAATTAGGCAGGCAGCTCGATGTTTCTTGGCAATTGGCGAGTACCATAATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCGGCTCCGTGGTCAACGAAGCCAGCCTTGGGAGCTTCATGGGTTACATGGCCCTTGCCCTGGGCAAGCTGTCCAACCTTGAAGGCTTTGTCATACAGgtgaagtccttgttgcctgccctttttccagttctgatccttctctccctgtttgactcaactttgtggatgtctagatgagcaatccaatcacttgaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc