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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccgagctcccctctccactccccctctctctgtttcagcttttttctttttttttaatccatgctgatttgtgatgcgagcatttgatttct...

Basic information

species Oryza sativa
transcript LOC_Os08g27090.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G108008_T01 (Zea mays), 5'ss of exon 1
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccga-gctcccctctc-cactccccctctctctgtttcagcttttttctttttttttaatccatgctgatttgtgatgcgagcatttgatttct
 ||||||||||||||| | ||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||| | ||   ||| ||||| |||||||||||||||||     ||| |    ||  |  | |||  ||   |||       | |     | |   |||    | || || |    | |   ||||| | |  
GGACCGCCTCTTCCACTATAAGATGTACAACCGCTATGTCAAGCGCACCTCTAAGTTCATGGCACACGACGAGGCTGACTCCTGCAACATTGGCGACCGGgtcggtaattattgctgcatcgtcgtatccgccccttcctcgttctgatgctgtaaggctgtgaaaattggcgatgcttagactggtgtcaatttgttat--

upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G177654_T01 (Zea mays), 5'ss of exon 1
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccgagctcccctctccactccccctctctctgtttcagcttttttctttttttttaatccatgctgatttgtgatgcgagcatttg-atttct-----
 ||||| ||||||||| ||||| | |||||||||||||||||||||||||||||||||||||| ||||| ||   |||   ||| ||||| |||||||||||| ||||     ||  |  || |  | |  |||   |  ||    |   ||    |||| | |  |  ||   ||| | ||||| | | | || |   ||     
GGACCGTCTCTTCCACAACAAGGTATACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCACACGACGATGACGACTCCTGCAACATTGGCGACCGGgtctgtaatt---cttgctccttcgattcgtctccaccccttc---cccgttctgattttgtaaggctgtggaaattagcgatgctaacttctgtaagactggtgt

upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA18G43720.1 (Glycine max), 5'ss of exon 1
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaac-cgagctcccctctccactccccctctctct----gtttcagcttttttctttttttttaatccatgctgatttgtgatgcgagcatttgatttct------------------------------------
 ||  | || ||| |||||||  ||||  | || || |||||||||||||| || |||||||| |||||||||| | |   ||||||||| || |||   ||  ||| |  || ||  |   |  | |     | |   |      || |  | || |   | || ||  |      |||||||| |  | | | ||||                                          
GGATAGACTTTTCTACCACAAATTGTATGATCGTTATGTCAAGCGCACCTCTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAAgttagtagcatgaacttacaattttatttggtttattcttcatcacttaaattcttgtgcatgttattcttatcacttgatttgt-actctaacttttgcccaaaagttaatgaatctatcaattttgtcatgttgtttag

upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA07G19190.1 (Glycine max), 5'ss of exon 2
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaac-cgagctcccctctccactccccct----ctctctgtttcagcttttttctttttttttaatccatgctgatt-tgtgatgcgagcatttgatttct------------------------------------------
 ||  | || ||| | |||||  | ||  | || || |||||||||||||| || |||||||| |||||||||| | |   ||||||||| || |||   ||  ||| |  |  ||  ||  |  | |     |     ||     || || | || |   | || ||  |     || ||    | ||  |  |  ||| |||                                            
GGATAGACTTTTCTATCACAAAGTCTATGATCGTTATGTCAAGCGCACCTCTAAATTCATGGCTCACGATGAGAACAACCTCTGTAACATTGGTGACAAAgttagtagcatggacttaccaatttaattggtttattgttcatcacttaagttcttgtgcatgttattcttatgatcttatcacttaatttgtactcttggttttgcccaaaagttaataaatctatcaattttgccatgttgtttag

upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G18880.1 (Arabidopsis thaliana), 5'ss of exon 1
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccgagctcccctctccactccccctctctctgtttcagcttttttctttttttttaatccatgctgatttgtga-tgcgagcatttgatttct----------------------------------------------------------------
|||| | ||||||||| | || || ||||| || || |||||||| || |||||||||||||| |||||||| |  ||   ||||||||||||||| || ||   |  ||         | |  | |     |   | || |  ||   |      |||    || |  |    || | |||   | | |||| ||  |                                                                  
CGACAGACTCTTCCACAATAATATCTACAATCGATATGTCAAGCGTACTTCCAAGTTCATGGCTCACGATGAAAAGGACTCCTGTAACATCGGCGATCGAgt-attttccccttcattttttgaatttgatatacatttgatcaagagctcgaaaatttagggaagctctaggaatatttgaactcaaccattggaagtagacttgcctgtttgttattaggctgctttggaaatgaaacttgatttggttgtttgaaatattag

upper sequence: LOC_Os08g27090.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G49400.1 (Arabidopsis thaliana), 5'ss of exon 1
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccgagctcccctctccactccccctctctctgtttcagcttttttctttttttttaatccatgc----tgatttgtgatgcgagcatttgatttct------------------------------------
|||  | ||||||||| |||| || ||||| ||||||||||| || || ||||| |||||||| ||||| || |  || | ||| ||||||||||| || ||   |   |  ||    |  ||   ||||  || ||||  ||  | ||  |||  | |||| ||||   ||    ||| ||  | |  | | |||  |  |||                                    
CGATAGACTCTTCCACAACAAAATCTACAATCGCTACGTCAAACGAACTTCCAAATTCATGGCTCACGACGACAAAGACGCCTGCAACATCGGCGATCGAgtaaattctctcgcatttccttc--ttccctttcactctaatttcgtttgattccgtcttttaaatctgagccacttgaattaggctttgtg-attgaacctctgaggctaagaaatttgaaaatctggttgatgtgtag

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|86419700|gb|CI054501.1|CI054501
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88219929|gb|CI219489.1|CI219489
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88218770|gb|CI218619.1|CI218619
EST:     ATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: ATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|86533796|gb|CI174002.1|CI174002
EST:     GGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: GGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|86508269|gb|CI150902.1|CI150902
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|87019649|gb|CI284335.1|CI284335
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88219930|gb|CI219490.1|CI219490
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88209745|gb|CI209594.1|CI209594
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88992130|gb|CI035268.1|CI035268
EST:     ATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCCAAAGGAAGCACTGGGTTGTT
genomic: ATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|86423680|gb|CI062441.1|CI062441
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|86509833|gb|CI152466.1|CI152466
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|44668586|gb|CR282020.1|CR282020
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGCAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88214879|gb|CI212917.1|CI212917
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
EST: gi|88219959|gb|CI219519.1|CI219519
EST:     CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGG                         GTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT
genomic: CCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTT

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), 69 (downstream exon)
Score: 33

CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaacc ... ttctctccagGTTAAGCTTGATCCTTCTAGGCCCTTGAGCAAAAGGAAGCACTGGGTTGTTGCCGAGATTCTTCGTAGAGCTAAGGTGTATTCTCCATCAGCTGCTGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACCGCCTCTTCCACCACAAGATGTACAACCGCTACGTCAAGCGCACCTCCAAGTTCATGGCGCACGATGAGACCGAGGACTGTAACATCGGCGACCGGgtcggtaaccgagctcccctctccactccccctctctctgtttcagcttttttctttttttttaatccatgctgatttgtgatgcgagcatttgatttct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccctc