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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtccccctctcctcctcctcaatgatgggggatattaaggtttccgttgattttggttttgcggcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g16190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G467059_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------gtcagtccccctctcctcctcctcaatgatgggggatattaagg--tttccgt-tgattttggttttgcggcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                                                         ||||    | ||||  |  || |     | |       |  ||   |  ||  || ||| ||  ||    ||  ||||||| ||||||||||||| |||||||| ||||| || |||||||| ||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||
gtgcgtagatcctccctctcttccccgtcccttccctgtaaccctagggtcagggactcagggttcgtctctgctccccccgctttcgttcgcgctcggggactgacgcgtggtttcggactt----cggtcgcagGGAGGGCCGGCGTGCCCATGGAGGTCATGGGTCTCATGCTCGGCGAGTTCGTCGATGACTACACCGTCAGGGTCGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033626_T01 (Zea mays), 3'ss of exon 1
----gtcagtccccctctcctcctcctcaat-----gatgggggatattaaggtttccgttgattttggttt----------tgcggcgcgc----------gcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
    ||   ||| |||  ||||| ||  |||     | | |||    |    |||| | ||   ||| | |           |  |  |||           |||||| |||| || ||||| |||||||| ||||| || |||||||| |||||||| |||||||||||||||||||| ||||||||||||||||||||||||||
gtgcgtggatcctccttccctcccccggaatctagggttagggttcgtccctgttttcctttgctttcgctcgcgctcggggtctgatgcgtcgtttcggttgcagGGAGGGCTGGGGTGCCCATGGAGGTCATGGGCCTCATGCTCGGCGAGTTCGTTGACGACTACACCGTCAGGGTCGTCGACGTCTTCGCCATGCCGCAGAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP09161 (Chlamydomonas reinhardtii), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------gtcagtccccctctcctcctcctcaatgatgggggatattaaggtttccgttgattttggtt--ttgcggcgcgcgca---gGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                                                                                                             | ||  |  | |     |  ||         |  | | || |    |||            |    ||  |    |||   || || ||||| ||||| |||||||| ||||| || ||| | || ||||| || ||||||||||| ||  ||||||| ||||| || || |||||||||  
gtaaggcgccgtgtttgcttgggtcctctgatagtagtgatgatgctacatcctggaggccgaccgcgagcgcttgaaggccctgcgctgcgaccccgtgtccagcttcggcacccagcttgcttgcaacccgtgcaccagcagctcttcaatcatccacccgcccactctgcccgcaacctttgcaatagGCCGCGCCGGTGTGCCCATGGAGGTCATGGGCCTCATGTTGGGCGAGTTTGTGGACGACTACACGGTGCGGGTGGTGGACGTGTTTGCGATGCCGCAGTC

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S146_35V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gtcagtccccctctcctcctcctcaatgatgggggatattaaggtttccgttgattttg-gttttgcggcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                             ||   |  | |||   || |   |    || | |     | ||| |  || |||   |  | |  |  || |||||  | || || || || ||||| |||||||| ||||||||||||||||| || ||||| ||||| ||  | || || || || || || ||||| |||||
tgttttttcacgtttggctatgtacacctagatgcaatatccctttcgtgcttatcaggaggtt----gatttgcactggtttcatgcctggacgttcgtgcagGTAGAGCGGGAGTTCCTATGGAAGTGATGGGACTGATGCTCGGGGAGTTTGTGGACGAGTACACTGTTCGTGTCGTAGATGTATTTGCTATGCCTCAGAG

upper sequence: LOC_Os01g16190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------gtcagtccccctctcctcctcctcaatgatgggggatattaaggtttccgttgattttggttttgcg-gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                             | |     |  | | ||| ||  ||   |||     |  | ||    ||| |      ||||   |  || |||||  | || || ||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||| ||  | || || || || || || ||||| |||||
tacattagggttcggtctattgtctaaagaatttaaatgacttgctcttcgttgggaggg----cttggattcaaattggtgacaaatttggacgatcgtgcagGTAGAGCTGGAGTGCCTATGGAGGTGATGGGGCTGATGCTTGGGGAGTTCGTGGACGAGTACACTGTTCGTGTTGTGGATGTATTTGCTATGCCACAGAG

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|55908865|gb|AU032022.2|AU032022
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|38480043|gb|CF964132.1|CF964132
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58678825|gb|CK067512.1|CK067512
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58678888|gb|CK067575.1|CK067575
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|38476931|gb|CF961064.1|CF961064
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|38478871|gb|CF963004.1|CF963004
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58691729|gb|CK080416.1|CK080416
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58598852|gb|CK009380.1|CK009380
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|568176|gb|D39011.1|D39011
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58679699|gb|CK068386.1|CK068386
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|6552265|gb|AU082093.1|AU082093
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58675840|gb|CK064527.1|CK064527
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58682525|gb|CK071212.1|CK071212
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|66926046|gb|CX112894.1|CX112894
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58677541|gb|CK066228.1|CK066228
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58680532|gb|CK069219.1|CK069219
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|218502937|gb|FG945477.1|FG945477
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCACGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58597372|gb|CK007900.1|CK007900
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58677827|gb|CK066514.1|CK066514
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|572299|gb|D41810.1|D41810
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
EST: gi|58675425|gb|CK064112.1|CK064112
EST:     CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACG                         GGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG
genomic: CGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCG

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: 75 (upstream exon), 56 (downstream exon)
Score: 10

GCGTCGGGGATGGGGCAGCCGCCGACGGACTCGCCGCTGCTCGACTCCTCCGAGCAGGTCTACATCTCCTCCCTCGCCCTCCTCAAGATGCTCAAGCACGgtcagtcccc ... gcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaatgatgggggatattaaggtttccgttgattttggttttgcggcgcgcgcagGGCGGGCCGGCGTGCCGATGGAGGTGATGGGGCTGATGCTCGGGGAGTTCGTCGACGACTACACCGTCAGGGTGGTCGACGTCTTCGCCATGCCGCAGAG
                          cgttgat  putative branch site (score: 10)
             atattaa  TA-rich tract