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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtatatttttcttattatatcccagccttgcatagttgcattccttgaatctactttgcatgttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G058948_T01 (Zea mays), 3'ss of exon 10
gtatgtatatttttcttattatatcccagcctt-gcatagttgcattccttgaatctactttgcatgttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
|| ||||| | | | |  |||| | | |||||| |||  | |  |    || || |||||||  || || |  ||||  ||  |  |||||||| || ||||||||||| ||||| |||||||||||||| || |||||||||||||| |||||||||||||||||||| ||||| |||||||| ||||
gtttgtat-tctatatgcttattttctagcctttgcactgct-taaaagttaaaactacttttgattttatggtacta-ctattcacagGCTGGGTTATCGATGGCACTTGGAGCTTTTTTGGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCCTTACAGGTTGAGTCAGATATAGCTCCTTATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G093643_T01 (Zea mays), 3'ss of exon 11
gtatgtatatttttcttattatatcccagccttgcatagttgcattccttgaatctactttgcatgttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
||  || | | | | |  |||| | | ||||||       | |||| ||| || ||||| |     |  |||||   |||  |  |||||||| || ||||||||||| ||||| ||||| |||||||| || |||||||||||||| ||||| || ||||||||||| ||||| ||||| || ||||
gttcgttt-tctatatgtttattttctagcctt-------tacattgcttaaaactactat-----tgattttatggtctattcacagGCTGGGTTATCGATGGCACTTGGAGCTTTTTTAGCTGGTCTGTTACTAGCAGAAACAGAGTTCTCATTGCAGGTTGAGTCAGATATAGCTCCCTATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G08030.1 (Glycine max), 3'ss of exon 10
-----------------------------------------------------------------------------------------------gtatgtatatttttcttattatatcccagccttgcatagt-tgcattccttgaatctac-------tttgcatgttgttttactct-ctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
                                                                                                | |||   ||    | || | ||  |    ||   | || |||   ||||   | |||       |||  |  |  |||| || | || |   ||||||||| | || |||||| |||| ||||||||||||||| || | || |||||||| || || |||||||||||||| || ||||||||||| || ||||
gtaggtgttcataccgatgttttttctttcccttatttccccttggtttgggtttttgagctaagccaaggtttgacagttttcaacagttattcttgtgtccgttgaagtgatgagatgacttttttttttggtgtgccaaccttacttttacccctttttttaaaaataatttttctttacttaaaacagGCTGGACTTTCCATGGCATTGGGGGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAGTTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA09G39770.1 (Glycine max), 3'ss of exon 14
----gtatgtatatttttctta---ttatatcccagccttgcatagttgcattccttgaatctactttg-catgttgttttactctctcattt----cagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
        || | |||||   |   || | | | ||    | ||  ||   ||| || |||  |  ||| | |||| || |  ||  | | ||    ||||| ||| | || |||||| |||||||||||||||||||| || | || |||||||| ||||| |||||||||||||| || |||||||||||||| ||||
gatgactggtctgtttttgaaaaccttgtgttcaagttcagtattttttagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCTTATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G46420.1 (Glycine max), 3'ss of exon 18
----gtatgtatatttttctta---ttatatcccagccttgcatagttgcattccttgaatctactttg-catgttgttttactctctcattt----cagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
        ||    |||||  |   || | | | ||    | ||  |||  ||| || |||  |  ||| | |||| || |  ||  | | ||    ||||| ||| | || |||||| |||||||||||||||||||| || | || |||||||| ||||| |||||||||||||| || ||||||||||| || ||||
gatgactggtccggttttcaaaaccttgtgttcaagttcagtatttttgagttcattaaattgatcttgacttgtttttgttttcctttacttaaaacagGCAGGACTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTACTACTGGCAGAAACTGAATTTTCCTTACAGGTTGAATCTGATATTGCTCCATATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT4G00630.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatgtat---atttttcttattatatcccagc---cttgcatagttgcatt-ccttgaatctactttgcatg--ttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
||||||     ||||| | | ||    |   |    || | |   |||| ||  |||   | |  ||   ||   ||||||   ||| | | || |||| ||| | || |||||| | ||||| ||||||||||||||| | || ||||| || ||||| ||||| || ||||| || ||||| ||||| |||||||
gtatgttcttgattttccgtgttggtgcttggtattctcgtaattttgctttgtcttttgtttcgttaagataaattgtttctttctttaaatt-agGCGGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTACTTGCAGAGACTGAATTTTCCTTGCAAGTTGAATCAGATATCGCTCCATACCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G01790.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgtatatttttcttattatatcccagccttgcatagttgcattccttgaatctac-tttgcatgttgttttactctct-catttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
||||| |   |   ||| ||       ||  | |  || |  ||| ||   | |   | | |||   || ||  | | |||  |  |||||||||| | || |||||| | ||||| ||||||||||||||| | || ||||| |||||||| || || || || || || ||||||||||| || ||||
gtatg-accgtgaccttgttggcattgag--tagtttactgacatgccagtacttcccgtctgctaatttttccagtttctataaatcagGCTGGACTTTCCATGGCATTAGGAGCGTTTTTGGCTGGTCTACTCCTTGCAGAGACAGAATTTTCGTTGCAAGTAGAATCAGATATTGCTCCATATCGTG

upper sequence: LOC_Os04g58620.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv15s0046g03390.t01 (Vitis vinifera), 3'ss of exon 9
gtat-gtatatttttc----ttattat-atcccagccttgcat------agttgcattccttgaatctactttgcatgttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
|||| | ||  |||||    ||||||| || |    |||  |       |||||  |  |     | | |||   |     |  |  |   | |   ||||| ||  | || |||||| |||||||||||||||||||| |  | || |||||||| ||||| |||||||||||||| || ||||||||||| || ||||
gtattggatgcttttcataattattattattcttttcttataccaatcaagttgtgtctcccttttttccttaagaaaaaatcatttttcttgaa--cagGCAGGCCTTTCCATGGCATTGGGAGCATTTTTGGCTGGTTTGCTTCTTGCAGAAACTGAATTTTCCTTACAGGTTGAATCAGATATTGCTCCATATCGTG

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|1631585|gb|C19314.1|C19314
EST:     GTCTTCTCACAGCTCGG                         GCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCA
genomic: GTCTTCTCACAGCTCGGgtatgtatat ... ctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCA




















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: 68 (upstream exon), 47 (downstream exon)
Score: 5

TCGTCCAATTTACAAGCAAATTGCTGAAAATAGGAACGCTGAGATATTTTCAGCAAATACTCTCCTTGTTATTTTTGGAACAAGTCTTCTCACAGCTCGGgtatgtatat ... ctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatagttgcattccttgaatctactttgcatgttgttttactctctcatttcagGCTGGATTGTCGATGGCACTGGGAGCATTTTTGGCTGGTCTATTGCTAGCAGAAACAGAATTCTCCTTACAGGTTGAGTCGGATATTGCTCCTTACCGTG
                                    ttttactctctcattt  CT-rich tract
                                 ttgtttta  TA-rich tract