Sequence
atgc intronic sequence ATGC exonic sequencegtagtttctgtcttcctctttaatcaaatgcaaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
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
|| | ||| || |||| | || | || | | || |||| || || | ||| | | ||||| || || || ||||| |||||||| || ||||||||| |||| |||||||||||||| ||||||||| || ||||||| || || || || || ||||
tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgattgcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCCMapped 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|CI752219EST: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTG
EST:
gi|33793273|gb|CF322517.1|CF322517EST: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAG GAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
genomic: ATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGA
EST:
gi|66913045|gb|CX099893.1|CX099893EST: 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:
30CGAGAACTTGGAAAATCCAGAGCTCTACCACTATGCACTTTTCTCAGACAATGTCTTGGCAGCATCTGTTGTTGTGAACTCAACCATAATGAATGCTAAGgtagtttctg ... accttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaactgtgataagtgataagtgttctgacaactatgtatggcataaccttttcagGAGCCTGAGAAGCATGTTTTCCATCTTGTGACTGATAAGTTGAACTTTGGAGCCATGAACATGTGGTTTTTGCTGAACCCACCTGGGAAGGCCACCATCC
ccttttc CT-rich tract
tatgtat TA-rich tract