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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTATGATATATGGTAGAGGACCAGCACCAGCTGGAATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataatgctgtcctagagtcacaactcacaaacaagtcttaccatacatcttcatttcctaacagttctgtttgtaatgtcttgacag

Basic information

species Oryza sativa
transcript LOC_Os10g06130.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g06130.5 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G103430_T04 (Zea mays), 5'ss of exon 8
CCTATGATATATGGTAGAGGACCAGCACCAGCTGGAATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataatgctgtcctagagtcacaactcac-------aaa---caa-----gtcttaccatacatcttcatttcctaacagttctgtttgtaatgtcttgacag
|| ||||||||||| |||||||||||||| || |||||||||||||| || |||||||| ||||| || || || || ||||| ||||||||  || |   |     || ||| |  |         ||   |||     | || | || | |||| || ||  | ||||     | |    | | | |||||
CCAATGATATATGGCAGAGGACCAGCACCGGCAGGAATGAGGATGGTGCCGATGGTGCTTCCTGATGGCCGCCTTGGCTATGTCCTgtaagaccattcctgcagtttgtgacagcatattctgcctgaagctcaatgtctgcctgagcacatatctgcagtttgtgacagcatattct----tctgtcgacag
















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|88903332|gb|CI088870.1|CI088870
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86899698|gb|CI327528.1|CI327528
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|89185712|gb|CI047581.1|CI047581
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88828403|gb|CI073273.1|CI073273
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGTATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86601473|gb|CI253801.1|CI253801
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCTGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|32948150|gb|BP184722.1|BP184722
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|29663247|gb|CB659522.1|CB659522
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86432190|gb|CI085801.1|CI085801
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTTTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGCCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|89180439|gb|CI044718.1|CI044718
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86540912|gb|CI181118.1|CI181118
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88271558|gb|CI387611.1|CI387611
EST:     ATGGTGCTCCCTGACGGTCGTCTGG-ATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88202330|gb|CI201192.1|CI201192
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88979541|gb|CI025979.1|CI025979
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88459812|gb|CI524271.1|CI524271
EST:     GTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: GTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|89185087|gb|CI049633.1|CI049633
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|33808242|gb|CF330010.1|CF330010
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|88968492|gb|CI098734.1|CI098734
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86869642|gb|CI322128.1|CI322128
EST:     ATGAGGATGGTACCAAT-GTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGT-GAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|89180350|gb|CI044629.1|CI044629
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
EST: gi|86910979|gb|CI294851.1|CI294851
EST:     ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCT                         GCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG
genomic: ATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCG

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), 68 (downstream exon)
Score: 54

CCTATGATATATGGTAGAGGACCAGCACCAGCTGGAATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataat ... gtcttgacagGCAACAACCAGGTGGAATCCCTCCTCCGCCCCCACCGCGTCGGGGTGACCGGAGGGATGGTGGCAGCAGAGGTGGCGAAGGGAGTCATGGCCGGCGATAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTATGATATATGGTAGAGGACCAGCACCAGCTGGAATGAGGATGGTACCAATGGTGCTCCCTGACGGTCGTCTGGGATATGTTCTgtaagataatgctgtcctagagtcacaactcacaaacaagtcttaccatacatcttcatttcctaacagttctgtttgtaatgtcttgacag

- - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - -  AGGATG