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

gtaaaccatccatccatccatccatccatcgattccttcctgaatgaatactggactagtaattcctaattattttttttcctcttcgtgtttctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA

Basic information

species Oryza sativa
transcript LOC_Os08g44340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G134708_T01 (Zea mays), 3'ss of exon 2
gtaaaccatccatccatccatccatccatcgattccttcctgaatgaatactggactagtaattcctaattattttttttcctcttcgtgtttc-tgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA
  |  |  | ||   || | || | |  || |||  |   |   |    |   | ||| |   |    |      |  ||    |   |  | | |  | |||||||| || || ||||| ||||| |||||||||||||||||||| |||||||
--atcctttacagaaatgcttcta-ctttcaattgttatatctgttcgcagctggctattctgtggcgacgccactgcttaacttcgatcctccatctttcagGTGGCCCCTTATGAGCGCCCTGCACTCAGCAAGGGATACCTCTTCCCTCAGA
















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:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATNAC-TCTTTCCTCA
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGAT-ACCTCTTTCCTCA
EST: gi|88721114|gb|CI744413.1|CI744413
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58591551|gb|CF989859.1|CF989859
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58670757|gb|CK059443.1|CK059443
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|33653794|gb|CF276408.1|CF276408
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88354143|gb|CI637709.1|CI637709
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58672555|gb|CK061241.1|CK061241
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|38568445|gb|CD670660.1|CD670660
EST:     CTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88717903|gb|CI739415.1|CI739415
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58689760|gb|CK078447.1|CK078447
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88722467|gb|CI745977.1|CI745977
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88408710|gb|CI686220.1|CI686220
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88363053|gb|CI616210.1|CI616210
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58665042|gb|CK053728.1|CK053728
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58594766|gb|CF993074.1|CF993074
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88575546|gb|CI669691.1|CI669691
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88408685|gb|CI686192.1|CI686192
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTNCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58599157|gb|CK009685.1|CK009685
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88330972|gb|CI638380.1|CI638380
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88586453|gb|CI704154.1|CI704154
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|29636698|gb|CB641707.1|CB641707
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58591384|gb|CF989692.1|CF989692
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTGCGGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88693460|gb|CI737035.1|CI737035
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|117233824|gb|CT847763.1|CT847763
EST:     CCAAGCAGGGCGTCAAACCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|58586261|gb|CF984569.1|CF984569
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGGGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88353573|gb|CI632964.1|CI632964
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|66912833|gb|CX099681.1|CX099681
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
EST: gi|88744711|gb|CI768071.1|CI768071
EST:     CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCG                         GTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG
genomic: CCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAG

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: 61 (upstream exon), 52 (downstream exon)
Score: 64

GGATACGCTGCGCGGGAGTTCGCCAAGCAGGGCGTCAAGCCCGGGGAACTCGCCATCATCTCCAAGGAATCGgtaaaccatc ... tctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactggactagtaattcctaattattttttttcctcttcgtgtttctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA
                tcctaat  putative branch site (score: 64)
                      ttattttttttcctct  CT-rich tract
         tagtaattcctaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccatccatccatccatccatccatcgattccttcctgaatgaatactggactagtaattcctaattattttttttcctcttcgtgtttctgctgcagGTGGCTCCCTACGAGCGTCCTGCTCTCAGCAAGGGATACCTCTTTCCTCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG