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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattatttatcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os04g55960.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G086489_T01 (Zea mays), 5'ss of exon 17
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattatttatcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
||||||| ||||| | ||||||||| ||||||| ||||||||||||||||| ||||| ||||| ||||||| |   ||||||||||| || ||||||||||||||  || |  | |  |   ||||| |   | | | ||||     | |     |||| |  || || |  | || |     |  || | |                       
GAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAATAGTCCAAGAGCAGgtagat-gacaaccgcaattcatcatctaatacgtgactatt----aacttcagtatgttg--tttgtaacatcttatttgtattttacctcag---------------------

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G053042_T02 (Zea mays), 5'ss of exon 1
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattatttatcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
||||||| ||||| | ||||||||| | ||| | ||||||||||||||||| ||||| ||||| ||||||| |   ||||||||||| || ||||||||||||||  || |  | |  |   ||||| |   | ||| |||      | |     |||| |  || || |  | || |     |  || | |                       
GAACATCATCTCAAATGGTGGTTACTTGTATATTTGCGGTGATGCCAAGGGAATGGCTAGAGATGTACACAAAATGCTTCATACAATAGTCCAAGAGCAGgtagat-gacaaccgcaattcatcatctaatacgttactata----aacttcagtatgttg--tttgtaacatcttatttgtattttacctcag---------------------

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G377451_T01 (Zea mays), 5'ss of exon 14
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattattta--tcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
|||| || ||||| | ||||||||| ||||||| ||||||||||||||||| ||||| | ||| ||||||| |   |||| |||||| || ||||||||||||||  || |  | |  |   ||||| |   | | | |||  |  ||     | || | | |||| |  | ||   ||             | | |  |                 
GAACGTCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTACAGATGTACACAAAATGCTTCGTACAATAGTCCAAGAGCAGgtagat-gacaaccgcaattcatcatctaatacgtgactataaacttcatacaatagttttggaatgaagcgtgccattgataatatactgaaatgagttg----------------

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G104294_T02 (Zea mays), 5'ss of exon 11
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattattta-tcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
||||||| ||||||| ||||||||| ||||||| ||||||||||||||||| ||||| ||||||||||||||    ||||||||| | || |||||||||||| | |      | |      || || | ||   ||||||  | |  | |  |   | |  ||    ||   | || |    || |                             
GAACATCATCTCACATGGTGGTTACTTATATGTATGCGGTGATGCCAAGGGAATGGCTAGAGACGTACACAGGATGCTTCATACAGTAGTCCAAGAGCAGgtacataac----cgcaacccatcgtctagatggctattatgaagtttactatgttgtttgtaac--atctcattttgtttcacttcag---------------------------

upper sequence: LOC_Os04g55960.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G480134_T01 (Zea mays), 5'ss of exon 7
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattattta-tcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag
||||||| ||||| | ||||||||| ||||||| ||||||||||||||||| ||||| | | | ||||| | |   ||||||||||| || ||||||||||||||  || |  | |  |   ||||| |   | | | |||  | |  ||  |    | | | |    | | || |     || |  ||  ||| | ||                 
GAACATCATCTCAAATGGTGGTTACTTATATGTTTGCGGTGATGCCAAGGGAATGGCTACATATGTACAAAAAATGCTTCATACAATAGTCCAAGAGCAGgtagat-gacaaccgcaattcatcatctaatacgtgactataaacttcatacaatagttttgga---atgaagtgtgccattgataata-tactgaaatgagttg-----------

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|15855705|gb|BI808517.1|BI808517
EST:     TATGGCAAGAGACGTACACAGAGCTCTTCATACCATTGTTCAAGAGCACG                         GGATCTTTGGATAGCTCCCAAACCGAGAGCTATGTAAAGAGCCTACAGAT
genomic: TATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCA-Ggtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGAT
EST: gi|88272817|gb|CI386077.1|CI386077
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCCAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|29674228|gb|CB670503.1|CB670503
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|88480979|gb|CI418250.1|CI418250
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|163929241|gb|EG712694.1|EG712694
EST:     GTATGGCGAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|88274984|gb|CI395588.1|CI395588
EST:     CATACAATTGTTCAAGAGCACG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGAT
genomic: CATACAATTGTTCAAGAGCA-Ggtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGAT
EST: gi|25800626|gb|CA756587.1|CA756587
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|86598832|gb|CI355449.1|CI355449
EST:     TACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: TACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|66917610|gb|CX104458.1|CX104458
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|33793723|gb|CF322744.1|CF322744
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|38480582|gb|CF964671.1|CF964671
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|88451326|gb|CI536719.1|CI536719
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCA-                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|88291090|gb|CI527480.1|CI527480
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|86872346|gb|CI323796.1|CI323796
EST:     CGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGTATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: CGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|88374287|gb|CI513374.1|CI513374
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|86883470|gb|CI338043.1|CI338043
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCA-                         GGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG
EST: gi|22307634|gb|BQ908856.1|BQ908856
EST:     GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAG                         GGATCTTTGGATAGCTCC-AAACCGAGAGCTATGTAAAGAGCCTACAGATG
genomic: GTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATG

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: 74 (upstream exon), 72 (downstream exon)
Score: 61

GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagag ... cttgtttcagGGATCTTTGGATAGCTCCAAAACCGAGAGCTATGTAAAGAGCCTACAGATGGACGGCAGGTACCTCCGTGACGTATGGTGACACCATCAGAATTATCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACATCGTCTCACAAGGTGGTTACATATATGTGTGCGGTGATGCCAAGGGTATGGCAAGAGACGTACACAGAGCTCTTCATACAATTGTTCAAGAGCAGgtagacagagagacactttgtctcatcaatatctttattatttatcgattgagagatgtcgaattagtcatgtattttcctgctcctaacacttacattttgcaccttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG