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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT

Basic information

species Oryza sativa
transcript LOC_Os03g10370.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G081622_T01 (Zea mays), 3'ss of exon 1
catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttacta-atattgcttgatgaggattcaacatatattcctttatat--gcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
   |||  |       ||| | |  | |   | |  |  |   ||      | |    |  |||  || |       |    | || |  |||| ||  |||| || || ||||||||||||||||||||||||||||||||||| ||||||||||||||||| || ||||||||    ||||||
---gtgcacttgtaaatggatgaactgatataatctaccgttcatttcgattcaaaggaccttgtctgcttgaataactgtttgtacttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCT

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G007188_T01 (Zea mays), 3'ss of exon 1
catgtgggccaacttctg-gtttatattagcgagtaaaatgga-tatgctttgttactaatattgcttgatgag--gattcaacatatattccttt-----atatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
          |||   ||    |  || | |   |  |||    |   | ||   | | |   ||||||       || | |  || | | | |||     || ||||| || || ||||||||||||||||||||||| ||| ||||||| |||||||||||||||||||| ||||||||   |||||||
---------taacacttgtaaatggatgaactgatgtaatcttctgctcctttcgattcaaggtgcttgcctgcttgaataactatttctgctttttttacatctgcagCCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCT

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA20G27070.2 (Glycine max), 3'ss of exon 1
catgtgggc-caacttctggtttatattagcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT------------------
  |||  |  | | |  |  || ||   |  |  | || || ||   | ||  || |   |||  |  |      ||   | ||   |  |  |     || || |||||||||||||| |||||| | || ||| | || |||||  |||||||||||||||| ||| | ||||| |||||                   
tgtgtatgttctattgatatttcattgaacaggattaattgaatg-accttcatagtggaatttgtaaacatttgtttctcttactcttgtccaatgatagCCTCTTTTTCAAGCAAGAAATGGAGTTATCTTTGGTTGGCCTTCAGGATGCTGGGAAAACATCACTTATAAATGTTATTGCAGTATCTTACCAGACCTTC

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT5G67560.1 (Arabidopsis thaliana), 3'ss of exon 1
catgtgggccaacttctggtttata---ttagcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
  |    |   | |    |   |     ||||      |||   |  |   ||| | |  || ||||  |||  | ||    |  | | | | |||| ||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || || ||||| ||||| || ||  |||| 
agtagatgaagattgtgagagcaagaacttagtttcccaaaaaaaagttgcttgcttcgcat-ttgcccgatatgcata-gtctcacaatgccttat-tgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCATTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTTAACGTTGTTGCA

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G49870.1 (Arabidopsis thaliana), 3'ss of exon 1
catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttactaat--attgcttgatgagg-attcaac-atatattcctttata----tgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
         | |    | ||  |  ||   ||  | | ||| | |  || ||  |||||  ||   | |||  || ||||||   | | || |  |||     ||||| || || ||||||||||| ||||||||||| |||||||| ||||||||||| || || ||||| ||||| |||||  |||| 
-------ttctaacaatcgtaaaatttcatgaa-agattggttctttttggtatctaatttatgtttcgattcggtattcaattgtttgtttccatatgattttgcagCCTCTTCTTCAAGCAAGAAATGGAGCTTTCTTTGATAGGACTTCAAAATGCAGGAAAGACATCACTTGTAAATGTTGTTGCA

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s0601g00030.t01 (Vitis vinifera), 3'ss of exon 1
-catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttactaatattgcttgatgagga-ttcaacatat-attcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
 ||  |      ||   || ||||| ||    |      |  ||    | | ||| |    || ||| ||  | |  |||   |||   |  | |    |||| || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||||||||| ||||| |||||  |||| 
tcacatattatgacaa-tgttttattttctttat--gtctttattcattctcttattcccttttcttaatatgtagctcattctattgcttatatgatcgcagCCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 3'ss of exon 2
-catgtgggc-caacttctggtttatatta-gcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
  |   |    ||| || |  ||  | | | |    |  | ||| | || | |  || |  | |||    |    |||| |    | |    ||     |||| || || |||||||||||||||||||| ||  ||||||| || || || |||||||||||||||||||| ||||| ||||| 
ataaacgatttcaatttataattactgtgatgttgatggattgggt-tgatctcctaat--tcttgagctagtgtgattaattggagagagattgtgcggcagCCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCG

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S103_13V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------catgtgggccaacttctggtttata----------ttagcgagtaaaatggatatgctttgttactaatattg-cttgatgaggat-tcaacatat--attcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
                                                                           |||||  ||  | || | ||| |          || | || |   |  | |||  ||| |   ||||  || ||   ||  ||  |  |   |    |||  |  | || || || ||||||||||||||||||||| | || ||||||||| | ||||||||||| ||||| || || |||||||||||||| 
gtagatgtcaaccttggcctgtatgtattgctaagtctcgatttcgctgaattctcttgtggtgttttttcattttgtggctcatgtacttgcttacagaagatatacttggggattgttagtggtataatttctgtgtaatgctgactctgtgctgacatggatggaatggttctctcgtgtgtagCCTATTTTTCAAGCAAGAGATGGAGTTGTCTTTGATAGGGTTGCAAAATGCTGGCAAAACTTCTCTCGTGAATGTCATTGCG

upper sequence: LOC_Os03g10370.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S263_59V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------------------------------------------catgtgggccaa--cttctggttt-atattagcgagtaaaatggatatgct----ttgttactaatattgcttgatgaggattca--------acatata----ttcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
                                                                     |||| |       ||    |||| |      ||| | | | ||| ||||     ||| ||    | | | |    || ||| ||        || ||||    |  | |  | |||||||| |||||||| |||||||||||||| || ||||||||||| || || || || ||||| || || || ||||||||||| 
gtagttactgaatttctgtctgtccatgcgattaagattcaattacacaattttataatttttcttgttatgttgttttgtgctgtgagtttgacgccttcgaatcaga-ggacatgcgggcattggtatcggtttggttgctcgaagatgcaggctctgtacttatacggttctcatcctgtgcagTCTCTTTTTCAAACAAGAGATGGAGCTGTCTTTGATAGGGCTGCATAACGCCGGAAAAACCTCTCTCGTCAATGTCATTGCG

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|38470884|gb|CF955015.1|CF955015
EST:     GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAG                         TCNNNNNNNCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
genomic: GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAGgtacgctcgt ... ttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
EST: gi|88586362|gb|CI704059.1|CI704059
EST:     GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAG                         TCNNNNNNNCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
genomic: GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAGgtacgctcgt ... ttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
EST: gi|117230769|gb|CT854061.1|CT854061
EST:     GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAG                         TCNNNNNNNCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
genomic: GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAGgtacgctcgt ... ttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
EST: gi|58680551|gb|CK069238.1|CK069238
EST:     GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAG                         TCNNNNNNNCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC
genomic: GGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAGgtacgctcgt ... ttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGC

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: 64 (upstream exon), 74 (downstream exon)
Score: 26

CCGCCGCCACCACCACCCAGGGTCCCCGCTTCGTAGGCGAGGGGGGAGGAGGAGACGACGCCATGGGGTTCTGGGAAGCCTTCCTCAACTGGCTCCGCAGgtacgctcgt ... ttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT
                                      tattccttt  CT-rich tract
                                   atatattcctttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtgggccaacttctggtttatattagcgagtaaaatggatatgctttgttactaatattgcttgatgaggattcaacatatattcctttatatgcagTCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
catgtgg
- - - - - - cttctgg
- - - - - - - - - - - - - - - -agtaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacata