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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT

Basic information

species Oryza sativa
transcript LOC_Os08g25734.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 5
----gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaa--tttataattgt------ctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
    | |   ||||| || |  |||  |||||  |  |||  |||         | || ||| ||   ||||||||          |||  |||| ||   | | || ||||  |   | ||| ||||||||||| ||||||||||| |||||||||||||||||  |||| ||||| |||||||||||||||||||||||||||||||| |||||||| || 
gtatgcacattttcacttct--cactgtgctgcagtagaaagttacaacgccgcatgcgtgtcaaatcttataatttcaattagtccctgctgatttagcgtttcccttcaatctgaatacagCTTCTATGACCGTTCTGCTCCAATCTATACACAACCTCGACATCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAGGGA

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttata--------attgtctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
||||||||||| || |  |||  |||||  | || |  ||       |  | |||| | || |  ||        |||   ||||  |||| ||   |   || | ||  |   | ||| ||||||||||| | |||||||||||||||||||||||||||| |||| ||||| |||||||||||||||||||||||||||||||| ||||||||||| 
gtatgctttcacttct--cactgtgctgcagttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
gtatgcttt-caatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
|||   | |  |   | |  |   |        |   ||  |  | |||| ||   |   |  || |  || |  |  |||||   | |   ||     || | |   |||||||||||||| || ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| 
gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtc-tccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
|||   |  | ||||  | |  |   |     |||  | | |   |||| ||  ||     ||| |  || |  |  |||||   | |    |     || | |   |||||||||||||| || ||  ||||||| || || ||||| ||| | |||||||| || ||| | |||||||||||||| || || ||||| ||||||||||| 
gtaaattgcctatttg-atatatccatcatattgacaaatgt---atttcaatgatagtgttttgtggttctgatgtttatgtgttcatgcgttttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
--------gtatgctttcaatttttacaccttgc-tgtggctgaagattatggaatttgaagcatg--tgaatttataattgtctccttatgatataaaatataccatcaaaat--atctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
          |  |  |||   | || ||  ||  | | | |     ||    | |||    |||      |||| | ||   |   ||||||||| || |||    |  || |  |  ||||| ||||| ||||| ||  ||||||| || || ||||||||| | ||||| || || ||| | |||||||||||||| || || ||||| |||||||| || 
gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgat--gcagtttatgatattaa-tatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGC

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|87012877|gb|CI297104.1|CI297104
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29681077|gb|CB677352.1|CB677352
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|58606969|gb|CK035002.1|CK035002
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACGACGTTGCCT
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC-AC-TTGCCT
EST: gi|33681770|gb|CF310009.1|CF310009
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATA
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATA
EST: gi|29612859|gb|CB617872.1|CB617872
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|38472262|gb|CF956393.1|CF956393
EST:     GAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: GAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29671442|gb|CB667717.1|CB667717
EST:     TTTTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|88586416|gb|CI704115.1|CI704115
EST:     TCCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TCTCTATGACCGGTCTGCTCCAATTTATANACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29660395|gb|CB656670.1|CB656670
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCCTCGACACTTGCCTT
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACC-TCGACACTTGCCT-
EST: gi|58652879|gb|CK041559.1|CK041559
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACA
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACA
EST: gi|58675386|gb|CK064073.1|CK064073
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
EST: gi|88584775|gb|CI702352.1|CI702352
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAACCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGAC
EST: gi|86831383|gb|CI299441.1|CI299441
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTG
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTG
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAG                         TTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC
genomic: TTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCC

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), 75 (downstream exon)
Score: 764

AAGCTTACTTGTATGATGGTTACTGGGAAGACATTGGTACCATTGAGGCATTCTATAATGCAAATCTGGGAATAACGAAAAAGCCTGTACCAGATTTCAGgtatgctttc ... atatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
                    ttatgatataaaatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttataattgtctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT