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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtcaagattgatacacggttcagcagttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttttggccttgtgttgatatacaagattgtctaaatgatatattttttttctgttcttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g02590.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02590.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 3
gttgtcaagattgatacacggttcagcagttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttttggccttgtgttgatatacaagattgtctaaatgatatattttttttctgttcttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG
                                         || |||     ||     |  ||  || ||||  | ||  ||  | |      | | || | |  |   |  ||||| |   |  | || ||||||||||||   || |||||  |||  ||| ||||||| |||||||||||||| ||||| | ||||||||| |||||||||
-----------------------------------------gtttgtcccgatggaaaggcttggttgctttgtgcatgcatttttttttcctttcgactgatttgttcttgctttttttccccccgttggtagAACAAGGAGGCGACGGACCGCGTTGCCAGGTTATCCCTGTACTGCTGGATGGCTTCTTCTGCCTGTGCAGGTCTAGTTGAG
















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|218487592|gb|FG945521.1|FG945521
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|25798400|gb|CA754361.1|CA754361
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACNAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|88421294|gb|CI569139.1|CI569139
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAG
EST: gi|33799872|gb|CF325803.1|CF325803
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAG
EST: gi|218490956|gb|FG953067.1|FG953067
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|313084054|gb|HO213837.1|HO213837
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|86829554|gb|CI286745.1|CI286745
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGCATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|38480632|gb|CF964721.1|CF964721
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|84117673|gb|CD151440.1|CD151440
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTACTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|29687966|gb|CB684241.1|CB684241
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|33662420|gb|CF293387.1|CF293387
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|29687965|gb|CB684240.1|CB684240
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|58611378|gb|CK039090.1|CK039090
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTA
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTA
EST: gi|218482011|gb|FG963443.1|FG963443
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|38469451|gb|CF953582.1|CF953582
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG
EST: gi|58585983|gb|CF984291.1|CF984291
EST:     TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAG                         AACAAGGAGC-CACAGACCGGATTGTAAGGATATCCCGGTACTGCTGGATG
genomic: TCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATG

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: 67 (upstream exon), 73 (downstream exon)
Score: 126

TCCAAAAATGCGCTGCTCTCGACTTTCTTGTTCCTGGACCAATTTGTATGGTTGGGAAGAACAGGGATATACAAGgttgtcaaga ... ttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgatatacaagattgtctaaatgatatattttttttctgttcttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG
                 gtctaaa  putative branch site (score: 126)
                               ttttttttctgttctt  putative PPT
     atatacaagattgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtcaagattgatacacggttcagcagttgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgttttggccttgtgttgatatacaagattgtctaaatgatatattttttttctgttcttgctgctagAACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA