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'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgatgcttctaggatctaattactactgtgcaaatatgttatgtttgctgtatgccagaatttccactaactgtaaagcttatggccttatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGATGAATGGCTTGGGCAACCTGGTTCAGAAAACGCAAAGAAGTATCTACACA

Basic information

species Oryza sativa
transcript LOC_Os03g53750.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53750.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G171998_T01 (Zea mays), 3'ss of exon 10
-tgtgatgcttctaggatc-taattactactgtgcaaat-atgttatgtttgctgtatgccagaatttccactaactgtaaagcttatggccttatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGATGAATGGCTTGGGCAACCTGGTTCAGAAAACGCAAAGAAGTATCTACACA
 | |  | | | ||   |  |||  | | ||     |||  |||    | | |  |||||  || ||        |    ||   | |   ||| |||||||| |||   ||||  | || |||   |||||||| ||||||| | ||||||| |||||||| ||||||||||||||||| || |||||||||||| | ||||
ttttcttacatgtaatttggtaaagagtcctacatgaattgtgtaccttctaccttatgc--gagttatgttcttccactaattatgta-tcttgtgtaccagATATTAATATCTGATCCTTTCCGTAACCCTATCGCGAAAAAACTATATGACGAATGGCTGGGGCAACCTGGTTCAGAGAATGCAAAGAAGTATTTGCACA
















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|29638417|gb|CB643426.1|CB643426
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86851673|gb|CI315251.1|CI315251
EST:     AGTCTGCGAAGGATCTTATCCAAGTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|88836091|gb|CI371196.1|CI371196
EST:     GGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: -GTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|88840151|gb|CI079605.1|CI079605
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|29667391|gb|CB663666.1|CB663666
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86425269|gb|CI070366.1|CI070366
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86889816|gb|CI333467.1|CI333467
EST:     TTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: TTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|88260258|gb|CI362551.1|CI362551
EST:     TAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: TAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|29667390|gb|CB663665.1|CB663665
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|88835083|gb|CI370386.1|CI370386
EST:     TGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: TGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86835162|gb|CI346637.1|CI346637
EST:     CTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATC-GTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: CTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86865476|gb|CI330938.1|CI330938
EST:     CTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: CTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|88833082|gb|CI369972.1|CI369972
EST:     TAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: TAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|89180560|gb|CI044839.1|CI044839
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|27545833|gb|CA764023.2|CA764023
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
EST: gi|86831032|gb|CI295514.1|CI295514
EST:     AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGAT                         GTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT
genomic: AGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGAT

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: 49 (upstream exon), 27 (downstream exon)
Score: 1

GCTGCCTGAATGGGGGAGGTCAAATAAAACCTGCCAAAGGCCAGTCTGCGAAGGATCTTATCCAACTACTAGAGGATGTGTACATCCAAGATgtaagctagc ... tatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGATGAATGGCTTGGGCAACCTGGTTCAGAAAACGCAAAGAAGTATCTACACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctgtatgccagaatttccactaactgtaaagcttatggccttatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGATGAATGGCTTGGGCAACCTGGTTCAGAAAACGCAAAGAAGTATCTACACA
                     cactaac  putative branch site (score: 1)
             agaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgatgcttctaggatctaattactactgtgcaaatatgttatgtttgctgtatgccagaatttccactaactgtaaagcttatggccttatgtaccagGTATCGGTATCCAACCCCTTCGAGAACCCTATTGCGAAAAGATTATATGATGAATGGCTTGGGCAACCTGGTTCAGAAAACGCAAAGAAGTATCTACACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- tgatgct
- - - - - - - - - - - -actactg
- - - - - - - - - - - - - - - tgcaaat
- - - - - - - - - - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgtatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttatg