Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttagactcctttagcactcattaatatatttcactggcactcacttcaacatgtgaaacattgttcgattctcattttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGAACATGGGACTCCTAGATC

Basic information

species Oryza sativa
transcript LOC_Os01g15110.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G017329_T01 (Zea mays), 3'ss of exon 6
------------gtacttttagactcctttagcactcattaatatatttcactggcact-cacttcaacatgtgaaacattg--ttcgattctca--ttttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGA-ACATGGGACTCCTAGATC---
            || |||||| ||| | |||  |  |   | |   ||| |    |||    || || ||  |  |   |    |||  |   ||  |||  || ||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| || || ||||||||      ||| ||||||  |  ||||  ||| | |||   
gtaatttcagaagtccttttacacttcgttaatatcctagattcatttttaggaacaccattctccatcaaattgatgttcagattcactgaccaattttcttgctgcagATATGCTTGTTGCTCGTTATTTTCGGAGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCCTAAA----AGCTTGGAAGGCAGCTGGGGTTCCGAAATCTGA

upper sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120115_T01 (Zea mays), 3'ss of exon 6
gtactttta-gactcctttagcactc-attaatatatttcactggcactcacttcaacatgtgaaacattgttcgattctc-attttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGA-ACATGGGACTCCTA-GATC--
||| ||| | ||  ||||   ||||   |||||||  |  |    || |   ||     ||     ||   || |   | | ||||   | |||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || || ||||| ||      ||| ||||||  |  || |  ||| | ||||  
gtagtttcacgagcccttctacactttgttaatatcctagatc--cattttttttggattgctgttcagatttagtgacccgatttctcgctgcagATATGCTTGTTACTGGTTATCTTCGGCGTGGTCCTGCTCATAGTGATAATAGTACTTGCAGCATAAA----AGCTTGGAAGGCAGCTGAGGTTCCAATGATCGA
















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|300216044|gb|HO088670.1|HO088670
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|38477394|gb|CF961527.1|CF961527
EST:     AAGGCCAACTCTCGAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|88502344|gb|CI429850.1|CI429850
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGGTGGTCCTGCTCATAGTGATAAT
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTC-GGGGTGGTCCTGCTCATAGTGATAAT
EST: gi|29666448|gb|CB662723.1|CB662723
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGCCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|58613206|gb|CK040918.1|CK040918
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|58680591|gb|CK069278.1|CK069278
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|88504172|gb|CI431678.1|CI431678
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTNTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|86593942|gb|CI260171.1|CI260171
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTC--A-TGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|58693969|gb|CK082656.1|CK082656
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|58696002|gb|CK084689.1|CK084689
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|88218005|gb|CI217854.1|CI217854
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|29662791|gb|CB659066.1|CB659066
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|88216094|gb|CI215943.1|CI215943
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|88200203|gb|CI200053.1|CI200053
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
EST: gi|29662790|gb|CB659065.1|CB659065
EST:     AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTG                         ATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC
genomic: AAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATC

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), 71 (downstream exon)
Score: 59

TGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAAAAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCTGgtacttttag ... tatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGAACATGGGACTCCTAGATC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actggcactcacttcaacatgtgaaacattgttcgattctcattttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGAACATGGGACTCCTAGATC
     cactcac  putative branch site (score: 59)
                                    ttctcatttt  putative PPT
                                         attttatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttttagactcctttagcactcattaatatatttcactggcactcacttcaacatgtgaaacattgttcgattctcattttatgttgcagATATGCTTGTTGCTGGTTATATTCGGGGTGGTCCTGCTCATAGTGATAATCGTCCTCGCAGCCTAGGCAGCAGCCTGGAAGAACATGGGACTCCTAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC