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'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataatgattttgtgaggaaaatatcccttctttcgacctttcatggtaggattatggacatgaaagttaactgaatataggttgtttaactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA

Basic information

species Oryza sativa
transcript LOC_Os01g01710.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 3
---------------------------------------gtataatgattttgtgaggaaaatatcccttctttcgacctttcat--ggtaggattatggacatgaaagttaactgaatataggttgt--ttaactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA
                                        | |    |  | |  ||  |  ||| |  |  || || | || |    ||| ||| |     ||| |        || | | || ||   || ||||  ||||| |||||||||||||| ||| | |||||||||||||| || ||||||||||||||  | || |||||||| |||||||| ||   ||||||||||||||
gtacagtgatgttttgagtatattcttttctttatgtccttttttcaagctcgaaagagatttatacacttgtttgaacattaaacaagtaagataaaaactatgcactcattgagagttttggatgcaattgacta--cagGTCAAAACATTCAAACCTAAGTTGGTTGCTGTAAGAAACGAATCATTAGTTGATGAATTGAAAGAAGCCTTGGCTGATTGCGAAGAGAAGCCAGAAATTA

upper sequence: LOC_Os01g01710.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G036290_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------gtataatgattttgtgaggaaaatatcccttctttcgacctttcatg--gtaggattatggacatgaaagttaactgaatataggttgtttaactaa--gcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA
                                          |||    |  |||  ||  || | | |  || || || | || ||   | | ||  |   | ||| |  | |  |||  ||      | ||||| |   ||||| ||||||||||| || ||| | |||||||||||||| ||  ||||||||||||| ||||| ||||| ||||||||||| ||   ||||||||||||||
gtacaatgatgttctgagtagattcttttctttttgcccttttattcaaagcttgaaagagaattttgcactcatttgagcattaatcttgcaagacaaaaaatatgcac-tcatttgagcattctggatgtaacttactacagGTCAAAACATTCAAGCCTAAGTTGGTTGCTGTAAGAAACGAAACATTAGTTGATGAACTAAAAGAAGCTTTAGCTGATTGCGAAGAGAAGCCAGAAATTA
















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|38474648|gb|CF958781.1|CF958781
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58607529|gb|CK035562.1|CK035562
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58689337|gb|CK078024.1|CK078024
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|86905401|gb|CI285364.1|CI285364
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|33676538|gb|CF304777.1|CF304777
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29613664|gb|CB618677.1|CB618677
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29620639|gb|CB625650.1|CB625650
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29688464|gb|CB684739.1|CB684739
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58667396|gb|CK056082.1|CK056082
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29681868|gb|CB678143.1|CB678143
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTATCTGATCAG                         GAGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58688271|gb|CK076958.1|CK076958
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58608359|gb|CK036392.1|CK036392
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29617049|gb|CB622061.1|CB622061
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|88311639|gb|CI574856.1|CI574856
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCCAAAG
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACC-AAAG
EST: gi|33663679|gb|CF294646.1|CF294646
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29620626|gb|CB625637.1|CB625637
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58607277|gb|CK035310.1|CK035310
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58588201|gb|CF986509.1|CF986509
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|29620641|gb|CB625652.1|CB625652
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|33381852|gb|CF197195.1|CF197195
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58658820|gb|CK047500.1|CK047500
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|88367566|gb|CI568338.1|CI568338
EST:     GTTGTTGCCTCTTGCTGCTGGCTCCAACTGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GTTGTTGC-TCTTGCTGCTGGCTCCAA-TGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58688021|gb|CK076708.1|CK076708
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58589270|gb|CF987578.1|CF987578
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58690161|gb|CK078848.1|CK078848
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
EST: gi|58604657|gb|CK015185.1|CK015185
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGT
EST: gi|58654652|gb|CK043332.1|CK043332
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATT
EST: gi|58671429|gb|CK060115.1|CK060115
EST:     GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAG                         GTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT
genomic: GGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTT

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: 70 (upstream exon), 71 (downstream exon)
Score: 73

ACATTGGACATAGTTGCGGAGAATCCAGATAAATTCCGGGTTGTTGCTCTTGCTGCTGGCTCCAATGTGACTCTTCTAGCTGATCAGgtataatgat ... aactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtaggattatggacatgaaagttaactgaatataggttgtttaactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA
                                         gtttaac  putative branch site (score: 73)
                                          tttaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataatgattttgtgaggaaaatatcccttctttcgacctttcatggtaggattatggacatgaaagttaactgaatataggttgtttaactaagcagGTGAAAACATTCAAACCAAAGCTTGTTGCTGTAAGAAATGAGTCATTAGTTGATGAGCTAAAGGAAGCCTTAGCTGATTGTGATTGGAAGCCAGAAATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG