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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC

Basic information

species Oryza sativa
transcript LOC_Os09g36190.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G386971_T01 (Zea mays), 3'ss of exon 7
gtagtttctgtcttcctctttaatcaaatgca-aactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
||| ||| || | | | ||| |||| | || || | | |||| | |||| |||||| | ||||||||| || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||||||||| |||||||||||||
gtattttgcgtgtactt--ttagtcaattattcaattgcactccactaagtagtttctaatggtgatgtttggcatgtctttttcagGAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCCACCATCC

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G379577_T01 (Zea mays), 3'ss of exon 7
gtagtttctgtcttcctctttaatcaaatgca-aactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
||| |||| | | | ||| |||| | || || | | | || ||| |||| ||| || ||||||||| | || ||||| ||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||| |||||||||||||||| ||||| |||||||
gtattttccatgcactt--ttagtcaattattcaattgcattcctcaaagtagttcctaacattgatgtttggaatgtccttttcagAAACCAGAGAAACATGTTTTCCATCTTGTGACTGACAAGTTAAACTTTGGAGCCATGAACATGTGGTTTCTGCTGAACCCACCTGGCAAGGCTACCATCC

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------------------------------------------gtagtttctgtcttcc-tctttaatcaaatgcaaactgtgat-aagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
| |||| || | | || | | | | | | | | || || | | | | | | | || | | | | || ||||| ||| ||||||||| || || ||||| |||||||| | || ||||||||||||||||||||||||||| |||| || ||||| || || || |||
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
-----------gtagtttctgtc----ttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgta--tggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
| || ||| | ||| | || | | ||| | | | | | | | || | |||| ||| || | | | | || ||||| ||| ||||||||||| || ||||| || ||||| | || |||||||||||||||||||||||| | | ||||| |||| || || || ||||
gcaccaaaaatatcgtgcatgtgaaagtgtatctatgatttagt--aaattat-acttttaaaaccaggcctcataactttgttattgtcttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------------gtagtttctgtcttcctctttaatcaaatgcaaactgtgat-aagtgataagtgttctgacaactatgtatggcata-accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
| |||| | | | || | | |||| | | | | || || | | | | | | || | | | | || |||| ||| ||||||||| || || ||||| |||||||| | || ||||||||||||||||||||||||||| |||| || ||||| || || || |||
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------------------------------------------------------gtagtttctgtc----ttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
| || ||| | ||| | || | | | | | || | | | | | || | | || | | | || ||||| || |||| ||||||| || ||||| |||||||| | || ||||||||||||| |||||||||| | | ||||| ||||| || || || ||||
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaaaaccaggcctcataact-tagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G46480.1 (Arabidopsis thaliana), 3'ss of exon 3
gtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttctga--caactatgtatggcataacctttt--cagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
| | | |||| | || ||| ||| ||||||| | | | || | | | ||| ||||| ||| | |||||||||||| ||||||||||||||| | ||||||||||| |||| ||||||||| || ||||||| ||||| | || |||||||
------------gtaatgatcaatccc-tagtaattgttgcaag-aataagtgctttaaacttacaaggcctactgggtttatttggcagGATCCTTCAAGGCATGTTTTCCACCTTGTGACTGATAAGCTCAACTTTGGAGCAATGAGTATGTGGTTTCTGTTGAACCCTCCTGGAGAAGCGACCATCC

upper sequence: LOC_Os09g36190.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
-----gtagtttctgtcttcctctttaatcaaatgcaaactgtgataa-----gtgataagtgttctgacaactatgtatggcataacctt----ttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
|| | ||| || |||| | || | || | | || |||| || || | ||| | | ||||| || || || ||||| |||||||| || ||||||||| |||| |||||||||||||| ||||||||| || ||||||| || || || || || ||||
tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgattgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

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|88728709|gb|CI752219.1|CI752219
EST:     ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG                         GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
EST: gi|33793273|gb|CF322517.1|CF322517
EST:     ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG                         GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
EST: gi|66913045|gb|CX099893.1|CX099893
EST:     ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG                         GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA

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: 60 (upstream exon), 32 (downstream exon)
Score: 30

CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
                                              ccttttc  CT-rich tract
 tatgtat  TA-rich tract