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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATCCCTCGCCCGCTCTTCCTCCGCCTCGTCTGCCACGCCCTCGCCCTCTACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctctctctcttcttctatttctaacatttcttctcttcagatcccccatgcttcttctctactggagtaatacatattcttcttcttttctttggttag

Basic information

species Oryza sativa
transcript LOC_Os09g39870.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G017334_T01 (Zea mays), 5'ss of exon 2
TCATCCCTCGCCCGCTCTTCCTCCGCCTCGTCTGCCACGCCCTCGCCCTCTACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctctctctcttcttctatttctaacatttcttctcttcagatcccccatgcttcttctctactggagtaatacatattcttcttcttttctttggttag
|| ||||  |    |||||||||  |||||||  | |||||||||||||||||||||| || |||||| |||||||| | ||||||   |  |||||||||||   |   | | | | | ||        |  |||| |   |   || |   ||        | | |||    ||||  |       | | |   ||||     
TCCTCCCAAGGGACCTCTTCCTCGACCTCGTCCTCGACGCCCTCGCCCTCTACAAGTACGTTGCCCCCAACCAGCGCGCCGATCTCATGCTCGCCTGCAGgtccgtccgccacacctttcctgccctcctctcttctgccactgcaattcaagatttcctcattttgctgagaaaataattgaaaaattccctcattttg-----

upper sequence: LOC_Os09g39870.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G048553_T02 (Zea mays), 5'ss of exon 2
TCATCCCTCGCCCGCTCTTCCTCCGCCTCGTCTGCCACGCCCTCGCCCTCTACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctctctctcttcttctatttctaacatttcttctcttcagatcccccatgcttcttctctactggagtaatacatattcttcttcttttctttggttag---
 ||     | |   |||  ||||  ||||| |  | |||||||||||||||||||||  ||||||||| |||||||| | ||||||   |  |||||||||||   |   |     ||| |     |        |  | |||    ||| ||   ||||   ||| |    | ||| || |  |  ||  ||||  |  |  |    
CCAGGGACCTCTTCCTCGACCTCGTCCTCGACCTCGACGCCCTCGCCCTCTACAAGTTCGTCGCCCCCAACCAGCGCACCGATCTCATGCTCGCCTGCAGgtcagtccaaccgcactctccccccccc----ccccccccctt----tcctcccctcttcccttctgccactgcaattcaaaaacccctcattttgctgagaaaataa
















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|58612669|gb|CK040381.1|CK040381
EST:     TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAG                         GATCCGGGAAAGGAAGGAATCAGTCACCATTCTTCTCTGCGGAACCAGCGG
genomic: TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAAGGAAGGAATCAGTCACCATTCTTCTCTGCGGAACCAGCGG
EST: gi|58668260|gb|CK056946.1|CK056946
EST:     TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAG                         GATCCGGGAAAGGAAGGAATCAGTCACCATTCCTTCTCTGCGGAACCAGCG
genomic: TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAAGGAAGGAATCAGTCACCATTC-TTCTCTGCGGAACCAGCG
EST: gi|58658382|gb|CK047062.1|CK047062
EST:     TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAG                         GATCCGGGAAAGGAAGGAATCAGT
genomic: TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAAGGAAGGAATCAGT
EST: gi|88364608|gb|CI612423.1|CI612423
EST:     TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGGAG                         GATCCGGGAAA
genomic: TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAA
EST: gi|58654746|gb|CK043426.1|CK043426
EST:     TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAG                         GATCCGGGAAAGGAAGGAATCAGTCACCATTCTTCTCTGCGGAACCAGCGG
genomic: TACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAAGGAAGGAATCAGTCACCATTCTTCTCTGCGGAACCAGCGG

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: 12 (upstream exon), 73 (downstream exon)
Score: 2

TCATCCCTCGCCCGCTCTTCCTCCGCCTCGTCTGCCACGCCCTCGCCCTCTACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctct ... ctttggttagGATCCGGGAAAGGAAGGAATCAGTCACCATTCTTCTCTGCGGAACCAGCGGCTGCGGCAAGTCTACTCTTTCCACCTTGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATCCCTCGCCCGCTCTTCCTCCGCCTCGTCTGCCACGCCCTCGCCCTCTACAAGTATGTCGCCCCCGACCAGCGCTCTGATCTCCACCGAGCCTGCAGgtctccctctctctcttcttctatttctaacatttcttctcttcagatcccccatgcttcttctctactggagtaatacatattcttcttcttttctttggttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG