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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggatgcttcctgttttccgattgccgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT

Basic information

species Oryza sativa
transcript LOC_Os02g10310.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G093359_T01 (Zea mays), 3'ss of exon 11
----------------------------------------------------gtaaggatgcttcctgttttccg-attgc-cgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
                                                        |||||   ||  |   ||  | |||   |    || ||||| | |  |   |  |    | ||  || ||| | |||  | ||||||||||||  | || ||||| ||| ||||||||||| | |||||||||||  |||| || |||||||| ||||||||||||||||| || ||||||
gtaagtacactgctgattcggttttttttcactttaaatgctcatgtgttttagttggatgtaacccatcaaccatactgcatatgattttgccata-gcacataaca-ttggcacattgttgaaaccaatttc-cacagGTATTGGACGGTGACGCAGCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT

upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G093359_T02 (Zea mays), 3'ss of exon 10
gtaaggatgcttcctgttttccg-attgc-cgtttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
    |||||   ||  |   ||  | |||   |    || ||||| | |  |   |  |    | ||  || ||| | |||  | ||||||||||||  | || ||||| ||| ||||||||||| | |||||||||||  |||| || |||||||| ||||||||||||||||| || ||||||
----ggatgtaacccatcaaccatactgcatatgattttgccata-gcacataaca-ttggcacattgttgaaaccaatttc-cacaggtattggacggtgacgcagCAGCTAACACACCACACTATCAATGGATGCAACATGAGGCCGGGGGATATATTTGCAACTGGCACACTCAGTGGACCT

upper sequence: LOC_Os02g10310.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G029566_T01 (Zea mays), 3'ss of exon 11
---------------------------------------------------------------------------------------gtaaggatgcttcctgttttccgattgc-cgtttcattaccatatgtatttgttagctttgtc---cttactgtaactattttttcc-cagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
                                                                                       || |  | | | ||   | | | |        |   || ||||| | |  |   ||   || |    ||  |||||| | ||||| | ||||||||||||  | |||||||| ||||||||||||||  | || ||||||||  |||| || |||||||| ||||| ||||||||||| || ||||||
gtaagcacactgcatattcgtttttttttcactttaaatactaacgtgtgctcctgcaccgttcgagaaaaagaaatactaatgtgtgttaataggatcccaactattcaaccatataatgttttgccata-gcacataacagtgctggcacatttcttgtaaccaatttttgcacagGTATTGGACGCTGACACAGCAGCTAGCACACCACACCATCAACGGATGCAACATGAGGCCGGGGGATATATTTGCGACTGGCACACTGAGTGGACCT

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|29660372|gb|CB656647.1|CB656647
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAATTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29672587|gb|CB668862.1|CB668862
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29612852|gb|CB617865.1|CB617865
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29657905|gb|CB654180.1|CB654180
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86599975|gb|CI258315.1|CI258315
EST:     AGGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTGACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: A-GGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29671043|gb|CB667318.1|CB667318
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCANNNNNNNNTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|163929432|gb|EG713401.1|EG713401
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|117232667|gb|CT861058.1|CT861058
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29637362|gb|CB642371.1|CB642371
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88904130|gb|CI006363.1|CI006363
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29672144|gb|CB668419.1|CB668419
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88691997|gb|CI735572.1|CI735572
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29643533|gb|CB648540.1|CB648540
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGGTTA-TGGATGCA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTG-TTAATGGATGCA
EST: gi|29636552|gb|CB641561.1|CB641561
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29636597|gb|CB641606.1|CB641606
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86496229|gb|CI138862.1|CI138862
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|29664840|gb|CB661115.1|CB661115
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88690598|gb|CI734677.1|CI734677
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|88223961|gb|CI223810.1|CI223810
EST:     AGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|86433902|gb|CI094245.1|CI094245
EST:     GAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: GAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
EST: gi|27548667|gb|CA766758.2|CA766758
EST:     AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCT                         GTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA
genomic: AAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAA

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), 59 (downstream exon)
Score: 49

GTCTGGATTAAGCCCAAGGAGCAAAGTGAACCATCAATGGTTGCAAAGAGTAACTTCAAGCATCTgtaaggatgc ... tttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcattaccatatgtatttgttagctttgtccttactgtaactattttttcccagGTATTGGACTTTAACACAGCAACTAGCACACCACACTGTTAATGGATGCAATCTGAGACCAGGGGATATGTTTGCAACTGGCACACTAAGCGGACCT
                                         ctattttttccc  CT-rich tract
         atatgtatttgtta  TA-rich tract