Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACCGAAATTGTCAAGGCTGATCTTGCCTCCAAGACATTGACCAGTTCAGCTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctcaactgtacctttaagctttaacccacaaagaaaagaggaatggtgttctttttagtaaattttggttgtgaacttgtaatgtttgtttat...

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G134708_T01 (Zea mays), 5'ss of exon 5
CACCGAAATTGTCAAGGCTGATCTTGCCTCCAAGACATTGACCAGTTCAGCTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctcaactgtacctttaagctttaacccacaaagaaaagaggaatggtgttctttttagtaaattttggttgtgaacttgtaatgtttgtttat
 || || ||||| ||||| || ||||| || |||||  |||||||| ||||||  | |||||| || ||||| || ||||||||||| || ||||||||||| |||||| |     |   ||       ||  ||       ||  ||||   |  |    |  ||   |  |  || || | |     |   |||| | 
TACTGAGATTGTGAAGGCCGACCTTGCTTCAAAGACTCTGACCAGTGCAGCTGCGGAAACCTTCACATATGAGACCTTGCTCATTGCTACGGGCTCCTCGgttagttcttactgaaattgttc--tccaaaaacatgttttcaatgggaaaacttgttacctgggt---tgctcattatgtattctgtcttcgtgttcag
















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|88344389|gb|CI677431.1|CI677431
EST:     CTGATGCAANCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCA
EST: gi|58591551|gb|CF989859.1|CF989859
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58670757|gb|CK059443.1|CK059443
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|33653794|gb|CF276408.1|CF276408
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTTCCACTGGCTCCTCG                         GTCATAGAGCTCACTGACTTNTGGTGTTCAAGGAGCAGAGGCCAACGACAT
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTT-TGGTGTTCAAGGAGCAGAGGCCAACGACAT
EST: gi|58672555|gb|CK061241.1|CK061241
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAG
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAG
EST: gi|38568445|gb|CD670660.1|CD670660
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58689760|gb|CK078447.1|CK078447
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58665042|gb|CK053728.1|CK053728
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58594766|gb|CF993074.1|CF993074
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACA
EST: gi|58599157|gb|CK009685.1|CK009685
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGGCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCA
EST: gi|88586453|gb|CI704154.1|CI704154
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGNTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCA
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58591384|gb|CF989692.1|CF989692
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|117233824|gb|CT847763.1|CT847763
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|58586261|gb|CF984569.1|CF984569
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|25797720|gb|CA753681.1|CA753681
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     TGATGCAACCTTTACCTTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: TGATGCAACCTTTACC-TATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
EST: gi|12404688|gb|AU166289.1|AU166289
EST:     CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCG                         GTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA
genomic: CTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATA

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: 74 (upstream exon), 74 (downstream exon)
Score: 82

CACCGAAATTGTCAAGGCTGATCTTGCCTCCAAGACATTGACCAGTTCAGCTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctc ... gcttgatcagGTCATAAAGCTCACTGACTTTGGTGTTCAAGGAGCAGAGGCCAACGACATATTGTACCTGAGGGATATTGAGGACGCTGACAAGTTGGTCGCGGCTATGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACCGAAATTGTCAAGGCTGATCTTGCCTCCAAGACATTGACCAGTTCAGCTGATGCAACCTTTACCTATGACACTTTGCTCATTGCCACTGGCTCCTCGgtgagttctcaactgtacctttaagctttaacccacaaagaaaagaggaatggtgttctttttagtaaattttggttgtgaacttgtaatgtttgtttat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa