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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggctggtttgatctttgtagttccctgtgacatttcatcagtgcctttagcacctcctaatttgtgaaattttccactag

Basic information

species Oryza sativa
transcript LOC_Os10g39220.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 5
ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggctggtttgatctttg-tagttccctgtgacatttcatcagtgcctttagcacctcctaatttgtgaaattttccactag
||| | || |||||||||||||||||||| ||||| ||||||||||| || ||||||||| | |||||||||||||| ||||||||||||||||| |    || ||||  ||| || |||  | || |    |||  | | ||   || || | || |||||| ||    | | |  |||
ATAATACAGCATGTGCTTCTAGATATGCCTGGGCTTGCATTCTTCACAACATATGCACTTCTAGTGCTCTTCTGGGCAGAGATTTATTATCAGgtac----ctcgttttgtctctgatagacctctctattgttttgttaatgttgtt-gcgcttcttaatttttgttcatgttctgtag

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 4
ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggctggtttgatctttgtagttccctgtgacatttcatcagtgcctttagcacctcctaatttgtgaaattttccactag
||| | |||||||||||||| |||||||||||||| |||||||||||||| ||||||||||| |||||||||||||| |||||||||||||||||  |    |  |||  ||| ||| |  ||   |    |||  ||| ||   || |  |||| |||||| ||    | | | ||||
ATAATACAACATGTGCTTCTGGATATGCCCGGGCTTGCATTCTTCACGACATATGCACTTTTAGTGCTCTTCTGGGCTGAGATTTATTATCAGgtatt----tctttttgtctctgttggacctc-tattgttttgtcaatgttgtt-gtgcctcttaatttttgttcctgttctctag

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA07G28990.1 (Glycine max), 5'ss of exon 4
ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgt--gctaggctggtttgatctttgtagttccctgtgacatttcatcagtgcctttagcacctcctaatttgtgaaattttccactag---------------------------------------------
||  |||||||  |  | || ||  ||||  | || || ||||| || || |||||||||||||| || |||||||| ||||||||||||||||   | | |  | ||      ||||    | | ||     |||      ||   ||  |  || | |  | |||   ||| |   | |                                             
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTATCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttcttccaggtagtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgctttttcag

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G01360.1 (Glycine max), 5'ss of exon 4
ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgt--gctaggctggtttgatctttgtagttccctg--tgacatttcatcagtgcctttagcacctcctaatttgtgaaattttccactag---------------------------------------------
||  |||||||  |  | || ||  ||||  | || || ||||| || || |||||||||||||| || |||||||| ||||||||||| ||||   | | |  | ||      ||||    | | ||  ||   |  |  | |||  |||   |   | |     |||   ||| |   | |                                             
ATTGTTCAACACATCTTGCTTGACGTGCCGAGTCTTGCTTTCTTTACAACATATGCACTTTTGGTCCTGTTCTGGGCTGAGATTTATTACCAGgcaagtttgatttgtggtgcatttgcttctacatggttggtttgcctcctgtgattttcttattccatggca-gtgtgttttgctgattggttttgatgggctgattactgcctcggtgttaaatgcttttgcag

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|29664023|gb|CB660298.1|CB660298
EST:     TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|218501789|gb|FG963428.1|FG963428
EST:     TCACGACGTACGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|29663945|gb|CB660220.1|CB660220
EST:     TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|218494016|gb|FG950655.1|FG950655
EST:     TCACGACGTACGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|218483378|gb|FG949318.1|FG949318
EST:     TCACGACGTACGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|87035684|gb|CI190306.1|CI190306
EST:     TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
EST: gi|29663981|gb|CB660256.1|CB660256
EST:     ATTTATTATCAG                         GCGGCGTGCAATTTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAA
genomic: ATTTATTATCAGgtgctaggct ... tttccactagGC-GCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAA
EST: gi|29659575|gb|CB655850.1|CB655850
EST:     TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAG                         GCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT
genomic: TCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAAT

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: 74 (upstream exon), 57 (downstream exon)
Score: 19

ATACTTCAACATGTGCTTCTAGATATGCCCGGGCTCGCATTCTTCACGACGTATGCACTTTTGGTGCTCTTCTGGGCCGAGATTTATTATCAGgtgctaggct ... tttccactagGCGCGTGCAATGTCCACTGATGGGCTTAGGCCAACTTTCTATTGGATCAATGCTGTGATCTATGCAATTCAG




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