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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagcccattttacttcataacaaaaaggaatagtattctgaattagttatgtctacgaggcatgaacactaggggcag...

Basic information

species Oryza sativa
transcript LOC_Os03g09250.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G155242_T01 (Zea mays), 5'ss of exon 4
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagcccattttacttcataacaaaaaggaatagtattctgaattagttatgtctacgaggcatgaacac-taggggcag
|||| || ||||||||||| || |||||||| || ||||| |||| ||||||||||||||||||||| || ||| ||||||||||||||||||| ||||||||||  |  ||| |||  |  | |||  |  | ||      ||   ||    |        || ||  ||   ||| ||     | | |  ||    || 
ATGATCCGGACTTCATCGCGGCTAACCAGGGCTCTCGCGCCAACAGTGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCAGgtatatggatatggatgctaacgtgcct-tggtgctaaggtgcacccagtgcaacctaaaacaaataaatactactatgaatttggtaaatatacatacat

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 5'ss of exon 4
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagc-ccattttacttcataacaaaaaggaatagtattctgaattagttatgt-ctacgaggcatgaacactaggggcag
|||| || |||||||||||||| |||||||| || || || |||||||||||||||||||||||||| || ||| |||||||||||||||| || ||||||||| | | |||| |||  |     |     |  | || |  |         |  | |  || ||  |   |  | || | | | ||  |    |    |  
ATGATCCGGACTTCATCGCCGCTAACCAGGGCTCTCGTGCCAACAATGTCATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAAGATATCAGgtattcggacatggatgctaacacacattggtgcaattaaagaagtgccctcagtgcagcctaaaacaaagaaatactgctatgaatttagtacatacac--

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G392513_T02 (Zea mays), 5'ss of exon 2
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagcccattt-tacttcataacaaaaaggaatagtattctgaattagttatgt-ctacgaggcatgaacactaggggcag----------------------------------------------------
|||| || ||||||| |||||| |||||||| || || || |||||||| ||||||||||||||||| || ||| ||||||||||||||||||| |||| |||| |  ||||  |||  |    |||  | |  | || |  |         |  | |  || |  |   | ||| | |  |   | |    ||    |||                                                     
ATGATCCGGACTTCAACGCCGCTAACCAGGGCTCTCGTGCCAACAATGTAATCAAGGGCACCAAGAAAGAACAGGTGGAGCAGATCATCAAGGATATCATgtattc-agcattgatgctaacatgcctttgtgcaattaaagaagtgtcctcagtgcaacctaacatgcctttgtgcaattaaagaagtgtcctcattgcaacctaaaacaaagaaatactgctatgaatttagtacatatacatatatatcag

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S55_204V6.1 (Physcomitrella patens), 5'ss of exon 3
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaa-----ttgagcccatt-ttact--------tcataacaaaaaggaatagtattc--tgaattagttatgtctacgaggcatg--aacactaggggcag
| ||||||||||||||||| || |||||||   | || ||||||||| ||||||||||  ||||||||||||| ||||||| ||| ||| |||||||  ||||  |   |||   ||  |      | | | ||||   |||        |  |  || |   |||||   |    | | |||   || | |  ||  |  |  |    | |  ||||
ACGACCCCGACTTCATCGCTGCTAACCAGGAGGCTCGTGCGAACAATCTCATCAAGGGTTCCAAGAAGGAGCAAATGGAGCGGATTATCCAGGACATACGgtactcatccatcactgagaagcttctcaacgcattaccactcgccgtgcttctgccacaggtgaataccttctggtaatttatgaatatttctgaatccagctatttttggttgcag

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S267_10V6.1 (Physcomitrella patens), 5'ss of exon 4
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagccca--ttttacttcataacaaaaaggaatagtattctgaattagttatgtctacgaggcatgaacactaggggcag----------------
| ||||| || ||||| || ||||||||||   | ||||| |||||| | |||||||| || ||||||||||| |||||| |||| ||| ||||||| |||||    | |         | |    ||      |||  | |      |  || |         ||||  |    || | | |   ||||  ||  || ||                 
ACGACCCTGATTTCATTGCTGCCAACCAGGAGGCTCGCGCCAACAATCTGATCAAGGGTACGAAGAAGGAGCAAATGGAGAAGATTATCCAGGACATTAGgtagggcgtccgattctatacttcttccgagccctacagcctgtttctagagagttacgg---aaattgatcgcatcgatgcg-tttgaatgctgaggtcaaaacattgtgattgcag

upper sequence: LOC_Os03g09250.2 (Oryza sativa), 5'ss of exon 4
lower sequence: EFJ37320 (Selaginella moellendorffii), 5'ss of exon 4
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagcccattttacttcataacaaaaaggaatagtattctgaattagttatgtctacgaggcatgaacactaggggcag
| |||||||| ||||| || |||||||| || || ||||| |||||  || |||| ||| ||||||| ||| |||||||  |||||||| |||||||||||||    | |     | || |     |    |  |||  |      | |   | |  |||     | |                                
ACGACCCCGATTTCATTGCAGCCAACCAAGGTTCTCGCGCAAACAACATCTTCAAAGGCTCCAAGAAAGAGAAGATGGATAAGATCATCGAGGACATCAGgtacttcgtcgaatctcgattgagttcttcctctctttcttttctcatgttttcgctttcatcccttgcag-----------------------------

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|29646112|gb|CB651119.1|CB651119
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGANCA-GGTGGTGGTGTTGTGGACTG
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGA-CAAGGTGGTGGTGTTGTGGACTG
EST: gi|58598823|gb|CK009351.1|CK009351
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|3760166|gb|C97424.1|C97424
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|59930133|gb|AB178675.1|AB178675
EST:     TCAYGGGCACCAAGACGGAGCAGATGGAGCAGATCATACA-GGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: TCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCAT-CAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|13420717|gb|AU174807.1|AU174807
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58675021|gb|CK063708.1|CK063708
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|58598555|gb|CK009083.1|CK009083
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|218487632|gb|FG964358.1|FG964358
EST:     CCAAGAAGGA-CAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAATGTGGTGGTGTTGTGGACTGC
genomic: CCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
EST: gi|29616445|gb|CB621457.1|CB621457
EST:     ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAG                         GGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC
genomic: ATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGC

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), 70 (downstream exon)
Score: 177

ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggc ... acttaaatagGGAGTTCAAGGAAAAGAGCAAAGTGGACAAGGTGGTGGTGTTGTGGACTGCAAACACTGAAAGGTACAGCAATGTCTGTGTTGGGCTCAATGACACAATG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGACCCCGACTTCATCGCCGCCAACCAGGGATCCCGCGCGAACAATGTCATCAAGGGCACCAAGAAGGAGCAGATGGAGCAGATCATCAAGGACATCAGgtatactggcatgcatggaattgagcccattttacttcataacaaaaaggaatagtattctgaattagttatgtctacgaggcatgaacactaggggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA