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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgagagcattttgttttag

Basic information

species Oryza sativa
transcript LOC_Os10g25130.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G088064_T03 (Zea mays), 5'ss of exon 8
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgt--tttgaatt-ctcagca------cattttcaatatggctgcattcatgctgcaccaaagcctaa--ttgagagcattttgttttag
|||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||||||||||||||||||||||  ||| | || |||||||       ||  || |||   ||  ||   ||   ||   |  |||||  | ||| |||| || ||| ||
GATGCAATTACTGATTAGGAATGAGAAAGATGGCATTCTGTGCCCAATTCCTCAGTACCCTTTGTACTCAGCCTCCATAGCTCTTCATGGTGGAGCTCTTgtatgtactttcatttgctcagcagaagaatatggtctatagtactaaatat-tgtatcaatgacacctaaaatcgagcgcatgttctttcag

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G17290.1 (Arabidopsis thaliana), 5'ss of exon 8
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgagagc-attttgttttag-----------------------------------------------
||||||  | || ||||     ||||||||||| || || || || |||||||| ||||| ||||||||||| || ||||| ||||| |||||| || | |||||||    || ||  |   ||  | |  ||  |    || | ||   || | | |  |   || |   | | ||| |                                                  
GATGCAACTTCTCATAACTTCAGAGAAAGATGGAATCCTTTGTCCTATTCCTCAGTATCCATTGTACTCAGCTTCAATTGCCCTTCACGGTGGAACTTTGgtatgttcgttat-ctttgtttatgatgatgatatc-attttgacgcattactatatcaaatgggaaaatgaatctgtctccaaagtttcttttgtctttcttctcattgtcgtcatgttcttctggtag

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G72330.3 (Arabidopsis thaliana), 5'ss of exon 8
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgagagcattttgttttag
||||||  | ||  | ||    ||||||||||| ||||| | ||| |||||||| ||||| |||||||| || || ||||| |||||||||||| || | |||||||    ||  ||| ||       | ||  | ||  ||  || | ||    ||  |  |||| |    |   | ||||
GATGCAACTTCTCTTGAGCTCAGAGAAAGATGGTATTCTTTCCCCGATTCCTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTGgtatgttc-atataatcatcatgg----agtaatgttgt-tttttggtaca----agttt--ttgaaatttgtacttcttag

upper sequence: LOC_Os10g25130.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 5'ss of exon 8
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttt-tgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgaga-gcattttgttttag----------------
|||||||||||||||||| |  ||||| ||||| ||||| || || |||||||| || ||||||||||| || || |||| ||| ||||||||  ||||||||||||| |  | | | ||  || |  |  ||   ||   ||  |  |     || |  ||| | | | |||  |  |   ||                
GATGCAGTTACTGATAAGAACGGAGAAGGATGGAATTCTTTGTCCCATTCCTCAGTACCCTTTGTACTCTGCTTCAATTGTTCTACATGGTGGCACTCTTgtatgtttgtataatataagagcaatagctgtaaacctttttttttttttttttaatgtgtaaataaaaagcacataataaaaggggggcaacccatgtc

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|157650406|gb|EX450040.1|EX450040
EST:     GTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: GTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|55411573|gb|CV723949.1|CV723949
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGTGTTTTTAGATCTCTGA
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGG-GTTTGGAGATCTCTGA
EST: gi|88269769|gb|CI381067.1|CI381067
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|29668876|gb|CB665151.1|CB665151
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|29667022|gb|CB663297.1|CB663297
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|29665582|gb|CB661857.1|CB661857
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|88412291|gb|CI573567.1|CI573567
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|157650043|gb|EX449677.1|EX449677
EST:     GTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: GTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|27553989|gb|CA997889.1|CA997889
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|33675102|gb|CF303341.1|CF303341
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAA
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAA
EST: gi|29666343|gb|CB662618.1|CB662618
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|29666342|gb|CB662617.1|CB662617
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGAC
EST: gi|33691675|gb|CF319914.1|CF319914
EST:     TCA-TATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGA
genomic: TCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGG-TGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGA
EST: gi|58684931|gb|CK073618.1|CK073618
EST:     CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTT                         GTCCCGTATTATCTTAATGAATCAACA
genomic: CTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACA

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), 73 (downstream exon)
Score: 195

GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttg ... tttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGACCTTAAGAAGCAACTCGAAGATTCTCGGTTGAAAGGCATTGATGTTAGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCAGTTACTGATAAGGAACGAGAAAGATGGCATTCTCTGCCCAATTCCTCAATATCCTTTGTACTCAGCCTCCATTGCTCTTCATGGTGGAGCTCTTgtatgttttgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgagagcattttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT