Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctcttttttttttatgtgacaaaaagatagtt...

Basic information

species Oryza sativa
transcript LOC_Os04g57400.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G464137_T03 (Zea mays), 5'ss of exon 4
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctcttttttttttatgtg-acaaaaagatagtt-
|||||| ||||||||||  || ||||| |||||||| || ||| ||||||||||||| | | ||||  |||| || ||||||||||| ||||||||||||||||| ||| || | || |||  |  || |     |   | | || ||  |  |   | |     ||  | |   |  ||||     |||   |  | | | 
CTATGGGCCAATGGGTTTTGATATTGGAGCCTTCCTTGGAAACCTGATTTTGGCATACTATGCACAGAATGGGCATGCTGATCAAGCGAATGATCGTAAGgtatgcatgaatctgttagct--tgttaattttgcaccctttataattccaagtctccaatggtagtattatacatggtttactcatacatgtacttggctt

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA20G26580.1 (Glycine max), 5'ss of exon 4
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattg-gctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctcttttttttttatgtgacaaaaag-atagtt
 ||||| ||||||||||  || ||||| || ||| |||| |||||||||||||| |  ||| | |||||||| || |||||||||||||||||||| || ||| ||     |||     |       | ||   |  |  |||   ||| |       | | |  |||  | |  |    ||   ||  |      ||| | 
TTATGGACCAATGGGTTTTGATATTGGAGCATTCTTGGGAAACTTGATTTTGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccctttttccatgtcttctgtggtcctt--acttgtcctcttctttgcatactatagttgttatttagtcacatttcttgttattctccataatc

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA10G40730.1 (Glycine max), 5'ss of exon 4
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattg-gctaataatagtaaatgaaagtgtgtacttttacc-tggtccacaaatgtcctcttttttttttatgtga-caaaaagatagtt
 ||||| ||||||||||  || ||||| || ||| |||| |||||||||||||| |  ||| | |||||||| || |||||||||||||||||||| || ||| ||     |||     |       | ||   ||      | |     |||  | ||    |  ||  | | ||||| ||  | |   | | ||  ||   
TTATGGACCAATGGGTTTTGATATTGGAGCATTCTTGGGAAACTTGATTTTGGCTTTCTTTGCTCAAGATGGGCATGCTGATCAAGCAAATGATCGAAAAgtaggtcccctttttccatgtcttctgtggtccttgtcctcttctttgcatactatagttgttatttggtcacatttttcttgttattctccataatcta---

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 4
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctctttttttt--ttatgtgacaaaaagatagtt--
 ||||| |||||||| |  || || || || ||  | || |||||||||||||| || ||| |||||||||| || ||||||||||  |||||| | || |||||| ||  ||  |    |  |     |  |||    |    | ||   |   ||    |||| |     | |   |  |   |||  ||     | |||  
TTATGGACCAATGGGGTTTGATATAGGCGCATTTTTAGGAAACTTGATTTTGGCTTACTTTGCACAAGATGGGCATGCTGATCAAGTGAATGATAGAAAAgtatgtctgtgttcttaacttcgtt----tctatggtttttcccatttccccaaagtttgaaaatatttagctgtccatagtctagtgttaattttcttgtttc

upper sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv03s0091g00100.t01 (Vitis vinifera), 5'ss of exon 4
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctg--gtccacaaatgtcctctttttttt--ttatgtgacaaaaagatagtt-
 ||||| |||||||| |  || || || || ||  | || ||||||||||||||||| ||| |||||||||| || | ||||||||  |||||| | || |||||| ||  ||       | ||     |   |     | |  | |||| ||    || |  |||| |     | |   |  |   |||  ||     | ||| 
TTATGGACCAATGGGGTTTGATATAGGCGCTTTTTTAGGAAACTTGATTTTGGCATACTTTGCACAAGATGGGCATGATGATCAAGTGAATGATAGAAAAgtatgtctgtgttctcaactttatttctatggtt-----tttccagttttccccaaagttctaaaatatttagctgtccatagtctagtgttaattttcttgttt

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|87019167|gb|CI297368.1|CI297368
EST:     TTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|8858194|gb|AU095512.1|AU095512
EST:     AAGCAAATGATCGTAAG                         NCTTACAAGAAATGGATCTTGAAGACCAATTGAAGATTTCATGGAATTTGT
genomic: AAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGA-CAATTGAAGA-TTCATGGAATTTGT
EST: gi|3767720|gb|AU031747.1|AU031747
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|66915549|gb|CX102397.1|CX102397
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|218504013|gb|FG946243.1|FG946243
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29674887|gb|CB671162.1|CB671162
EST:     TGGCATA-TTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29657873|gb|CB654148.1|CB654148
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29618688|gb|CB623700.1|CB623700
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29615261|gb|CB620273.1|CB620273
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|27576846|gb|CA999540.1|CA999540
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTG
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTG
EST: gi|29662561|gb|CB658836.1|CB658836
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29641347|gb|CB646354.1|CB646354
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|88359320|gb|CI679847.1|CI679847
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|88412647|gb|CI690393.1|CI690393
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|29626239|gb|CB631250.1|CB631250
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
EST: gi|88583470|gb|CI700952.1|CI700952
EST:     TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAG                         GCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC
genomic: TGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTC

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), 75 (downstream exon)
Score: 103

CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatgg ... tatttttcagGCTTACAAGAAATGGATCTTGAAGACAATTGAAGATTCATGGAATTTGTTCCACAAGAAGTTTGTCGAATTATGGAATAAACACAAAGATGGGAATGGGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGCCCAATGGGTTACGACATTGGGGCCTTCCTGGGGAACTTGATTTTGGCATATTTTTCACAAGATGGACACGCTGATCAAGCAAATGATCGTAAGgtatgtatggatttattggctaataatagtaaatgaaagtgtgtacttttacctggtccacaaatgtcctcttttttttttatgtgacaaaaagatagtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaga