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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaactttaccttctttttaaatcttactggacattttttgaataaacaggaagcagttcgaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG

Basic information

species Oryza sativa
transcript LOC_Os10g25130.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G088064_T03 (Zea mays), 3'ss of exon 7
gtaggaacttt-accttctttttaaatcttactggacattttttgaataaacaggaagcagttcgaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
||  | | ||| | ||||| ||| |||  | ||||||||||| |||||||||| ||      |  | ||||||  |||   |||||| ||    |  || |||| |||||||||||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||||||||||||||| ||||||||||
gtgtgcatttttaacttctctttcaattgtcctggacattttctgaataaacatgatatcactgaagtctcatcttgaccttattcttcc----ttcttaagGTCCACATGATGATGCAATTACTGATTAGGAATGAGAAAGATGGCATTCTGTGCCCAATTCCTCAGTACCCTTTGTACTCAGCCTCCATAGCTCTTCATG

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G72330.2 (Arabidopsis thaliana), 3'ss of exon 7
------gtaggaactttaccttcttttta-aatcttactggacattttttgaataaacaggaagcagttcgaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
       |   |||   | | |  | | | |   |||  | |  || ||| ||     ||||  ||     | | |  || || || | ||  | |       | ||||||||||||||||||||  | ||  | ||    ||||||||||| ||||| | ||| |||||||| ||||| |||||||| || || ||||| |||||||
gtaacaatcaaaacgaaaacgttatctcatagagttagagtaagttcttttaa-----aggattcatgctaagtgt--ttttggtgttttttactc-------tatagGTTCACATGATGATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATG

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 7
gtaggaactttaccttctttttaaatcttactggacattttttgaataaacaggaagcagttcgaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
                                | |  || ||| ||     ||||  ||     | | |  || || || | ||  | |       | ||||||||||||||||||||  | ||  | ||    ||||||||||| ||||| | ||| |||||||| ||||| |||||||| || || ||||| |||||||
--------------------------------gtaagttcttttaa-----aggattcatgctaagtgt--ttttggtgttttttactc-------tatagGTTCACATGATGATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATG

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaggaactttaccttctttttaaatcttactggacattttttgaataaacaggaagcagttc-gaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
||| | |  ||| |    |    |||||| || |  | |  | ||||    |  |    |||  |||  | |   ||||| |  |||||       || |||||||| |||||||||||  | || ||||     ||||||||||| || || || || |||||||| ||||| ||||||||||| || ||||| ||||| |
gtaagga--ttatcaaact----aatctt-ctcgtaactcgtagaatctggaacaccttgttttgaagttgacagtgatgttcctctcc-------ttctagGTTCATATGATGATGCAACTTCTCATAACTTCAGAGAAAGATGGAATCCTTTGTCCTATTCCTCAGTATCCATTGTACTCAGCTTCAATTGCCCTTCACG

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 7
---------------------gtaggaactttaccttctttttaaatctt--actggacattttttgaataaacagga----agcagttcgaatctcattat--gatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
                     ||      |||  |||  ||||  |||||  | ||   | |  ||||| |     ||    |  | ||| |   | | ||    ||| | ||||||| |||| | | |||| || ||||||||||||||||||||||| |  ||||| ||||| ||||| || || |||||||| || ||||||||||| || || |||| ||| ||||
gtaaatttcaatttctgttttgttttttttttttctttcttttgtatcttttaatgacaactaattgaaaatttgtgattttaaaatttcaagcataaataacaaatgtttttctccctctct-tatcagGTCCATATGATGATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATG

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|25799461|gb|CA755422.1|CA755422
EST:     ACCCTGCANATGCAGACCACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGGCA-TTACTGATNAGGAACGAGAAAGATGGCATTCT
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATG-CAGTTACTGATAAGGAACGAGAAAGATGGCATTCT
EST: gi|88361410|gb|CI605191.1|CI605191
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGGAACGAGAAAAGATGGCATTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGG-AACGAGAAA-GATGGCATTC
EST: gi|29667022|gb|CB663297.1|CB663297
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|29665582|gb|CB661857.1|CB661857
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|157652418|gb|EX452052.1|EX452052
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGG
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGG
EST: gi|157652409|gb|EX452043.1|EX452043
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGG
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGG
EST: gi|58691201|gb|CK079888.1|CK079888
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|157652426|gb|EX452060.1|EX452060
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATG
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATG
EST: gi|88412291|gb|CI573567.1|CI573567
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|27553989|gb|CA997889.1|CA997889
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|33675102|gb|CF303341.1|CF303341
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|29666343|gb|CB662618.1|CB662618
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|29666342|gb|CB662617.1|CB662617
EST:     TGCAAATGCAGACGACA-TTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: TGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
EST: gi|33691675|gb|CF319914.1|CF319914
EST:     CCCTGCAAATGCAGACGACATCTTCCTTACTGACGGAGCAAGCCCCTGGA                         GTTCACATGATGAATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTC
genomic: CCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCC-TGGAgtaggaactt ... tctgttttagGTTCACATGATGA-TGCAGTTACTGATAAGGAACGAGAAAGATGGCATTC
EST: gi|58684931|gb|CK073618.1|CK073618
EST:     ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGA                         GTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC
genomic: ACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTC

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: 211

CAAAGGGCTGCGTGATGCAATTGCTGCTGGAATTGCATCACGTGACGGATACCCTGCAAATGCAGACGACATTTTCCTTACTGACGGAGCAAGCCCTGGAgtaggaactt ... tctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacaggaagcagttcgaatctcattatgatgctattctccccctctgttttagGTTCACATGATGATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATG
                               tgctattctccccctc  CT-rich tract
                        attatgat  TA-rich tract