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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGACCACTTAATAGTTTTCCTTGGCCCAGAAAGGCTTGAGGCTTGAGAGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggacaatctttctctttttaggattctataaacgaatgtgtcctttcatagtttaatcattcatgaagaatgatgacatgagatttatttacttag

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 2
splice site 5'
intron type U2

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|117251528|gb|CT844202.1|CT844202
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|33682634|gb|CF310873.1|CF310873
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|66924263|gb|CX111111.1|CX111111
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|8857838|gb|AU095156.1|AU095156
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGGAAGGATTAAGAGAGTACAT
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTG-AAGGATTAAGAGAGTACAT
EST: gi|13422333|gb|AU176452.1|AU176452
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCA
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCA
EST: gi|11565271|gb|AU165907.1|AU165907
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTTGGACACTGAAGGATTAAGAGAG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGT-GGACACTGAAGGATTAAGAGAG
EST: gi|88370619|gb|CI590197.1|CI590197
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88431461|gb|CI579578.1|CI579578
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88356835|gb|CI619321.1|CI619321
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAGTGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88430193|gb|CI565206.1|CI565206
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGT-CATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88351304|gb|CI627320.1|CI627320
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58672423|gb|CK061109.1|CK061109
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58676983|gb|CK065670.1|CK065670
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88425369|gb|CI567089.1|CI567089
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|33676567|gb|CF304806.1|CF304806
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58674501|gb|CK063188.1|CK063188
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88377696|gb|CI605531.1|CI605531
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGGATTAAGAGAGTACAT
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGG-ATTAAGAGAGTACAT
EST: gi|29677102|gb|CB673377.1|CB673377
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58672650|gb|CK061336.1|CK061336
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|2312757|gb|C28912.1|C28912
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACAT
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGG-AATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACAT
EST: gi|58676963|gb|CK065650.1|CK065650
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58591906|gb|CF990214.1|CF990214
EST:     AGCTGAGAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|33800393|gb|CF326065.1|CF326065
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|58664289|gb|CK052975.1|CK052975
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|33795605|gb|CF323672.1|CF323672
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGNGATGTGGACACTGAAGGATTAAGAGAGTACAT
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGG-GATGTGGACACTGAAGGATTAAGAGAGTACAT
EST: gi|88414769|gb|CI604127.1|CI604127
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|88368494|gb|CI572703.1|CI572703
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|33684319|gb|CF312558.1|CF312558
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
EST: gi|86596647|gb|CI286560.1|CI286560
EST:     AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTG                         GTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG
genomic: AGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATG

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), 68 (downstream exon)
Score: 41

GAAAGACCACTTAATAGTTTTCCTTGGCCCAGAAAGGCTTGAGGCTTGAGAGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggac ... atttacttagGTTCTTGGAATCCCATGGGATGTGGACACTGAAGGATTAAGAGAGTACATGGGCAAGTTTGGACCCCTAGATGATTGCGTCGTCATGAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGACCACTTAATAGTTTTCCTTGGCCCAGAAAGGCTTGAGGCTTGAGAGCTGAAAAGTTCTGCTGGAGCTAGTGCTATAATGGCCACAAAACTTGTGgtaagtggacaatctttctctttttaggattctataaacgaatgtgtcctttcatagtttaatcattcatgaagaatgatgacatgagatttatttacttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT