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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctcccatttctgaaacaaatttctttttgttttgtgctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactag

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 10
AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaac-ctctcccatttctgaaacaaatttctttttgttttgtgct-gtattttgttgtttttccataccagtaacgtttctgcc--tcttatatttactag------------------------
||  |||||| || ||| |||||||||||||||||||||| ||||| ||||  || |||||||||||||||||||||||||| || |||   |||| ||| |     | |   | ||| | | |  |||||| || ||| | | | | |     |        ||| ||      || | |||| |                          
AATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAGgtattactcttccaatagaacagctgctgtctatgtttactgtgcttgtgtttggctttctatttgctcttaccttttttttgttagctttctttttattgtctaatttgtcttattttttttcag

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 10
AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctcccatttctgaaacaaatttctttttgttttgtgctgtattttgt----tgtttttccataccagtaacgtttctg--cctcttatatttactag--------
||| ||| || || |  |||| | | || | |||||| |||||||| ||||| || ||||||||||| ||||||||| |||  || |||      |   |  |  |||    |  ||||||  ||| |    |  ||| |    || |||  |||  || |||| | |      |  || | || |   |        
AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAGgtaggaaa-caattcgccaaaaattttccctttttactttatttatttgtttatgctttggtttggcatctcattaacttgtgaaaatcctttttgttcatctgctatgcag

upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ28907 (Selaginella moellendorffii), 5'ss of exon 9
----------------AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctcccatttctgaaacaaatttctttttgttttgtgctgtattttgttgtttttccataccagtaacgtttctgcctcttatatttactag
                 | | |||  ||   |||||| |  |||||||||||||||||| ||||||| |||||| || || ||||| ||| |  | || || || |  |     |  |   |   | | |  ||      ||    ||| |||| |  |||| |||                                  
CAATCACGATGAACAACATGAGGATGGGGCTATGCAATT--AGATGGTCCTGAAAACAATCCACAGTTCACGACAGTATACGTTGGTAATTTAGCGCACGAGgtcagttgaaggacataacagttacagtggttaagacgtt---ttgtgtttt-taattttcccag---------------------------------

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|218488516|gb|FG953157.1|FG953157
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|29641559|gb|CB646566.1|CB646566
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218492528|gb|FG964892.1|FG964892
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88690783|gb|CI734862.1|CI734862
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218488001|gb|FG950016.1|FG950016
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGNT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88689298|gb|CI732874.1|CI732874
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58688359|gb|CK077046.1|CK077046
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATG
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATG
EST: gi|58687280|gb|CK075967.1|CK075967
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTT
EST: gi|29640531|gb|CB645540.1|CB645540
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCCACAGCAATGATGTGCACAGATTTTTCCAT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCAT
EST: gi|87019113|gb|CI297314.1|CI297314
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|33680119|gb|CF308358.1|CF308358
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGGTTGGTTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGG-TTGGTTC
EST: gi|218498744|gb|FG958423.1|FG958423
EST:     GGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: GGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88691922|gb|CI735497.1|CI735497
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|88572117|gb|CI663688.1|CI663688
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGAT
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGAT
EST: gi|58587445|gb|CF985753.1|CF985753
EST:     CTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: CTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218482201|gb|FG960522.1|FG960522
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|218500911|gb|FG960833.1|FG960833
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58597389|gb|CK007917.1|CK007917
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCA
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCCACAGCCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGC-AATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTC
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTC
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTC
EST: gi|87004665|gb|CI300987.1|CI300987
EST:     AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT                         GTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGG
genomic: AAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGG

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), 62 (downstream exon)
Score: 92

AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGATgtaacctctc ... tatttactagGTCAACAGCAATGATGTGCACAGATTTTTCCATTCACTTGGGGTTGGTTCAATTGAGGAGGTGCGTGTAACGCGTGATAAAGGTTTTGGCTTTGTGCGTT




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