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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagactgtaacatatttctggtccacactccctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g23860.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G318942_T01 (Zea mays), 5'ss of exon 8
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag
||||||||||||||||   ||||||||| | || | |||||||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| || ||||| |||||| | | || ||     ||||| |||| |  || | ||| || ||    |   | || |||||||      | || |||||
AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatg-ttagcagaatgaacatttaacttcactgtttaaacattctactaaatttttctggctgtttcaccatgcag

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G117507_T01 (Zea mays), 5'ss of exon 11
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag
||||||||||||||||   ||||||||| | || | |||||||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| || ||||| |||||| | | || ||     ||||| |||| |  || | ||| || ||    |   | || |||||||      | || |||||
AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatg-ttagcagaatgaacatttaacttcactgtttaaacattctactaaatttttctggctgtttcaccgtgcag

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G077635_T01 (Zea mays), 5'ss of exon 1
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag
||||||||||||||||   ||||||||| | || | |||||||||||| ||||| ||||| |||||||||||||||||||||||||| |||||||| || ||||| |||||| | | || ||     ||||| |||| |  || | ||| || ||    |   | || ||| ||||     | || |||||
AATTGATCTACTTGGTTCTGTAGATGAGATTTTCTATGATATCTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCTCGACAgtaagatttgcagtttatg-ttagcagaatgaacatttaacttcactgtttaaacattctactaaatttttttggttgtttcaccgtgcag

upper sequence: LOC_Os05g23860.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G435373_T01 (Zea mays), 5'ss of exon 11
AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttgcaatatctgatttttgaaatgagcattaagtttgattgtctagac----tgtaacatatttctggtccacactccctgcag
||||||||||||||||   || |||||| |||| | |||||| ||||| ||||| ||||| |||||||||||||||||||||||||| |||||| |||| ||||| |||||| | | || ||  |  ||||| |||| |  || | ||| || ||    |   | || ||| |||      | || |||||
AATTGATCTACTTGGTTCTGTGGATGAGATATTATATGATATTTATGACAGATATGAACCAGTGAATGAACCATCTCTTGATAATTGCTTTGTCACAACGgtaagatttgcagtgtatg-ttaatagaatgaacatttaactttactgtttaaacattctactaaatctttgtggctgtttcaccgtgcag

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|86871470|gb|CI342070.1|CI342070
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|9865466|gb|AU101216.1|AU101216
EST:     GATACGAACCTGTGAATGAACCATCTCTTGNTAATTGTTTTGTCNCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86840415|gb|CI342592.1|CI342592
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86260596|gb|CI066469.1|CI066469
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88842172|gb|CI081428.1|CI081428
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86435660|gb|CI106893.1|CI106893
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|10794783|gb|AU108749.1|AU108749
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88840787|gb|CI080241.1|CI080241
EST:     GATACGAACCTGTGAATGAACCATCTCTCGATAATTGTTTTGTCTCGACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|89177786|gb|CI390965.1|CI390965
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86869296|gb|CI339020.1|CI339020
EST:     TTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: TTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88841305|gb|CI080759.1|CI080759
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88262293|gb|CI366067.1|CI366067
EST:     ACGAACCGGTGAATGAACCATCTCGTGATAATTGGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: ACGAACCTGTGAATGAACCATCTCTTGATAATT-GTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88850115|gb|CI091410.1|CI091410
EST:     TACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: TACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88829029|gb|CI073899.1|CI073899
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88199358|gb|CI199208.1|CI199208
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88830963|gb|CI080387.1|CI080387
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86251492|gb|CI016781.1|CI016781
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88837944|gb|CI371522.1|CI371522
EST:     CCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: CCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86428756|gb|CI075437.1|CI075437
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACA                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88845153|gb|CI084078.1|CI084078
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88243406|gb|CI244528.1|CI244528
EST:     AATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: AATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88975224|gb|CI023475.1|CI023475
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88834169|gb|CI000533.1|CI000533
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86435740|gb|CI106973.1|CI106973
EST:     CCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: CCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88840911|gb|CI080365.1|CI080365
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86870784|gb|CI323828.1|CI323828
EST:     CCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: CCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88733192|gb|CI756369.1|CI756369
EST:     TTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: TTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|88842404|gb|CI081660.1|CI081660
EST:     ATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: ATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|27920752|gb|CB096560.1|CB096560
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|25797461|gb|CA753422.1|CA753422
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|86836554|gb|CI348415.1|CI348415
EST:     TAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: TAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|89177785|gb|CI390964.1|CI390964
EST:     CGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTTTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: CGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
EST: gi|27920430|gb|CB096238.1|CB096238
EST:     GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACT                         AGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC
genomic: GATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAAC

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), 75 (downstream exon)
Score: 53

AATTGATCTACTTGGTCAAGTAGATGAGCTATTTTTTGATATCTATGATAGATACGAACCTGTGAATGAACCATCTCTTGATAATTGTTTTGTCTCAACTgtaagttttg ... ctccctgcagAGCTATGATGCCACCACACATTTTGAGACAACGGTGACAGATGTTCTTAACATGTATACATTGATCACCGGAAAG




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