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

gtgagatttgaataaaagacatttatgtgtttcctgattttgtaacctcattataatagtttactgtgtgttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG

Basic information

species Oryza sativa
transcript LOC_Os03g38960.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G086904_T01 (Zea mays), 3'ss of exon 5
gtgagatttgaataaaagacatttatgtgtttcctga------ttttgtaacctcattataatagtttactgtgtgttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGAC-TGAGGCTACTCAAAACGAACAG---
||||||||  |   |||  ||  ||  | |||  |        ||||  ||  |  | ||  |   ||||| ||| || ||| |  ||||||| |||||||| || |||||||| |||||||||||||||||||||||||||||||| || | || |     |||  |   |||||    | | | ||   
gtgagattccatggaaaagcacatacttcttttttatgaatacttttacaatgtagtcatctttaattactttgttttaaaaca--gCTATGAAGACTGGGGAGTAGACGAGCTCATTGTGGAGGACTCCTGGAAACGCCAGGTTGGTGGAGACTGAA----GACGCGGATCTACTTGGCATGGAAAGGGT

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G013600_T01 (Zea mays), 3'ss of exon 5
gtgaga---tttgaataaaagacatttatgtgtttcct--gattttgtaacctcattataatagtttactgtgt-gttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG---
|||||    ||  ||| |||  |  | |  | |||      |   | | ||   ||| | || ||| | |   | ||| | | | || ||||| |||||||| || |||||||| |||||||||||||||||||||||||||||||| || | || |   |   ||||  |||||    | | | ||   
gtgagtattttctaatgaaaagccctcacttatttttatgaacaattttactatattttcattgttaattacttcgttgataaacagTTATGAAGACTGGGGAGTAGACGAGCTCATTGTGGAGGACTCCTGGAAACGCCAGGTTGGTGGAGACTGAA--GATGCTGAT-CTACTTGGCATGGAAAGGAT

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G013600_T02 (Zea mays), 3'ss of exon 5
gtgaga---tttgaataaaagacatttatgtgtttcct--gattttgtaacctcattataatagtttactgtgt-gttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG
|||||    ||  ||| |||  |  | |  | |||      |   | | ||   ||| | || ||| | |   | ||| | | | || ||||| |||||||| || |||||||| |||||||||||||||||||||||||||                                             
gtgagtattttctaatgaaaagccctcacttatttttatgaacaattttactatattttcattgttaattacttcgttgataaacagTTATGAAGACTGGGGAGTAGACGAGCTCATTGTGGAGGACTCCTGGAAACGCCAG---------------------------------------------

upper sequence: LOC_Os03g38960.1 (Oryza sativa), 3'ss of exon 5
lower sequence: EFJ06023 (Selaginella moellendorffii), 3'ss of exon 5
gtgagatttgaataaaagacatttatgtgtttcctgattttgtaacctcattataatagtttactgtgtgttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG
                            || |  | | |  || | |   ||       ||    |  |  |    | |||||| ||||| |||||||| |||||||| ||||||||||| || |||||  | || ||||||  |                                    
----------------------------gtatgttaagtgagtgatcctcttcgcgcgtttctaagaattcttgcttctagCTACGAGGATTGGGGCGTAGACGAGCTGATTGTGGAGGATTCTTGGAAGAGACAAGTTGGAAACTAG---------------------------------

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|218495985|gb|FG958579.1|FG958579
EST:     AGAGCACGCAAGATCCCATTCACCATTACGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCT
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCT
EST: gi|88376199|gb|CI533101.1|CI533101
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTNTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88215899|gb|CI215748.1|CI215748
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|86506229|gb|CI148862.1|CI148862
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218497334|gb|FG955294.1|FG955294
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88517263|gb|CI444917.1|CI444917
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|58681466|gb|CK070153.1|CK070153
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|38481397|gb|CF965486.1|CF965486
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218496317|gb|FG954187.1|FG954187
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|25798016|gb|CA753977.1|CA753977
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGGAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218487224|gb|FG954426.1|FG954426
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218491289|gb|FG948708.1|FG948708
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTG
EST: gi|86416666|gb|CI030677.1|CI030677
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|86536627|gb|CI176833.1|CI176833
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218490022|gb|FG965705.1|FG965705
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88216290|gb|CI216139.1|CI216139
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|163928871|gb|EG711933.1|EG711933
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218498533|gb|FG957594.1|FG957594
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|86507172|gb|CI149805.1|CI149805
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|163917777|gb|EG711299.1|EG711299
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88518337|gb|CI445991.1|CI445991
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTNTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|218484046|gb|FG946740.1|FG946740
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGG
EST: gi|88907433|gb|CI090227.1|CI090227
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|58686251|gb|CK074938.1|CK074938
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTA
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTA
EST: gi|163920983|gb|EG710396.1|EG710396
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88289429|gb|CI555791.1|CI555791
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|88323979|gb|CI561388.1|CI561388
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|38468521|gb|CF952652.1|CF952652
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|15851727|gb|BI800003.1|BI800003
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
EST: gi|86911562|gb|CI296648.1|CI296648
EST:     AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAG                         CTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG
genomic: AGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACG

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: 34 (upstream exon), 46 (downstream exon)
Score: 61

ATTGCCATGAAAGAGCTGAGAGCACGCAAGATCCCATTCACAATTAGGCGGTACTTACCTGACGGAAGgtgagatttg ... tcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtttcctgattttgtaacctcattataatagtttactgtgtgttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG
             ttgtaac  putative branch site (score: 61)
                     tcattataatagttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatttgaataaaagacatttatgtgtttcctgattttgtaacctcattataatagtttactgtgtgttcaaatatagCTATGAGGACTGGGGCGTTGACGAGCTTATTGTGGAGGACTCCTGGAAACGCCAGGTTGGAGGCGGCTAAGCTGTGACTGAGGCTACTCAAAACGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG