Sequence
atgc intronic sequence ATGC exonic sequenceATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt...
Basic information
species | Oryza sativa |
transcript | LOC_Os02g07870.1 |
intron # | 17 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G128877_T04 (Zea mays), 5'ss of exon 1
---------------------ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaat-----tttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt
||||||||||| ||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||| ||||||| |||| | ||| | ||| |||||| | | ||| | | | | | ||| | || | | ||| ||| || |
ACAAGTGTTGTTTAATATTAGATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaa--cttctgattgt---
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G128877_T02 (Zea mays), 5'ss of exon 17
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaat-----tttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt
||||||||||| ||||||||||||||||| ||||||||||||||||| |||||||| |||||||||||||||| ||||||| |||| | ||| | ||| |||||| | | ||| | | | | | ||| | || | | ||| ||| || |
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAATATTATTCACTTCAACACATTGGCAAATCAGgtaagctctcaactagcagtacttctgtaatttttgagtaaatgtttttcctgcagattgttttgcaatgatcaaggaaacttattaaa--cttctgattgt---
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GRMZM2G421857_T02 (Zea mays), 5'ss of exon 17
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaacttt-ccaataattgt
||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||||| ||||||| ||| | | || | | | | | | | || | || || | ||| ||||| | ||| ||| | |||
ATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAGgtaaggtctttaatgcccacccccctgttttgtaaccaatcaattatcacaatttattgttgctccacctgctatcattgtattgttttgtcaagatttg-
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgcca-attttctttaga---aaaccaatcctagctgactagaaaatcat--gccaaaactttccaataattgt
||||||||| | |||||| |||||||| |||||||||||||||||||||||||| |||||| ||| ||||||| |||||| | || |||||| | | ||| |||| |||| | || || | | | | |||||| || | ||| | | | |
ATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatgg----tagtgtaaggaatcaggcagtttttggtgttttatttatactagaaaaaagaagaaaagtccatgtaatcattggcatctaggttcaagttact--
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgcca-attttctttaga---aaaccaatcctagctgactagaaaatcat--gccaaaactttccaataattgt
|||||| || | ||||| |||||||| |||||||||||||||||||||||||| |||||| ||| ||||||| |||||| | || |||||| | | ||| |||| |||| | || || | | | | |||||| || | ||| | | | |
ATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAGgtatgg----tggtgtaaggaatcaggcagtttttggtgttttatttatattagaaaaaagaagaaaagtccatgtaatcattggcatctaggttcaagttact--
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt----
|||||| |||| ||| || || ||||| || |||||||||||| | ||||||||||||||| | | ||||| | |||||| | | || |||| || | || | | | | | || || | | |||||| || | | | | ||| |
ATATGACAAGTTTTGTCCCTTTTACAAGTCAGTTTGGATGATGAGGAACATTATTCATTTCTATAATTTGGCCAATCAGgtac-tcttatttttccctttctttcctgatatttcctctctatgtattct-tcatttttttctgactcaaagg--gtatctgattggacaaatgaaaagaaaa
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgta-aattctcttgttccaggaattcgataat---ttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt-
||||||||||| ||||| |||||||| || ||||||||||||||||| ||||| |||||| | | ||||| | |||||| || || | | | ||| | | || ||||| || |||| | | | | |||||| | | | |||
ATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAGgtacgatgttcctctctctctctttccaccccccctcccccgttttcctttttctctttgaccta--ttgttgtcatgtt-tgccaagatcatt--gtgtctgta
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaattttctttagaaaaccaatcct-agctgactagaaaatcatgccaaaactttccaataattgt-------------------------------------------------------------------------------
||||| || | |||||||||||||| ||||| ||||||||||| || ||| | || |||||||| | |||| ||||| || || ||||| ||| | ||| | || ||||| | | | | ||| | ||| || ||| |||| | |
TTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAGgtttgctcg-ttattccaa-aatgtttttgtttattatttatcttttcctcctcttttttgaattgattcattaatt-tgttaaatctttgagttgttcaaattttgatgattgggtggttgtatctcaactcgtatgtttacaaattccaaaactaatgagcgatgatttcatctgcag
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgataatttgccaatt--ttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt-
|||||||| | ||||||||| || || || || |||||||||||||||||| | || |||||||| | || | ||||| || || ||| |||| | | || || || | | || | ||| | | || || | ||| |
TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAGgt---ctcgttttgcccataaattttaatgtgcatcagttagttttgtttgttacttgttttagtggtgaatgtgatgatttttatgtattctcgcacggaat
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 18
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctcttgttccaggaattcgata-atttgcca--attttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt
|||||||||| ||||||||||| ||||| || |||||||||||||| ||| | || || ||||| | || | ||||| |||||| || | | | || | ||| || | || || | | | | || | ||| |||| | | | || ||
TTATGATAAGTTCTGCCCATTCTATAAATCAGTATGGATGATGCGCAATATTGTCCACTTTAACACTCTTGCCAATCAGgtct-ttctctcactcgattcttactgtacagttggcatcaagtttttccggtcattactgctcttcaattagttgttcatatcttgatcaac--atgtttac
upper sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 17
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 17
ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattct------cttgttccaggaattcgataatttgccaattttctttagaaaaccaatcctagctgactagaaaatcatgccaaaactttccaataattgt
||| ||||||| ||| || |||||||| || |||||||||||||| ||||| |||||||| | || | || |||||| || | | || || | | || ||||| | ||||| | | |
ATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAGgtatgcactgccatacctctttcacgtccttgaaaattt----actttctcttgcag-------------------------------------------------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|86829584|gb|CI286768.1|CI286768EST: CTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG GCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
genomic: CTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctc ... tgttttatagGCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
EST:
gi|89198392|gb|CI007452.1|CI007452EST: CTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG GCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
genomic: CTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctc ... tgttttatagGCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
EST:
gi|88956459|gb|CI092711.1|CI092711EST: TTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAG GCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
genomic: TTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctc ... tgttttatagGCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTC
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:
73 (upstream exon),
65 (downstream exon)
Score:
11ATATGATAAGTATTGCCCATTCTACAAATCTGTTTGGATGATGCGCAACATTATTCATTTCAACACATTGGCAACCCAGgtaaattctc ... tgttttatagGCGGTGGAGCGGGCAGCTGGTGCTGATGGACAGAAGATTACATACAGTGTCATAAAGCATCGCATGGGCGATCTATTCTACCGCCTAGT
<
<
<