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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTATCTACTTCCTCTACCTCCCCTAATCCACTCCACTCCACCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaacttgccaacggggattctctccgaccgattcaccgggatttctcccgcggtcgccgctccacccatgttttttttttttttgggttcttgcttgtccgtccctgacgaatgttgcaatggtgtttcttggctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g29860.1
intron # 1
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|29675291|gb|CB671566.1|CB671566
EST:     CCTCAAATTCTCCCGCGGCTAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCCCTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88667078|gb|CI719214.1|CI719214
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|87017421|gb|CI287961.1|CI287961
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88905625|gb|CI712924.1|CI712924
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|87011172|gb|CI287849.1|CI287849
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88594406|gb|CI714364.1|CI714364
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|33682562|gb|CF310801.1|CF310801
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88594629|gb|CI714587.1|CI714587
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88905107|gb|CI712406.1|CI712406
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88973494|gb|CI717922.1|CI717922
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|33686568|gb|CF314807.1|CF314807
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88675096|gb|CI729209.1|CI729209
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88904956|gb|CI712255.1|CI712255
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88738022|gb|CI761530.1|CI761530
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88676991|gb|CI731104.1|CI731104
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88908777|gb|CI714919.1|CI714919
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88667588|gb|CI722327.1|CI722327
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88431710|gb|CI576901.1|CI576901
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|11565230|gb|AU165866.1|AU165866
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|58685345|gb|CK074032.1|CK074032
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCAGCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGCGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88669978|gb|CI724094.1|CI724094
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88954949|gb|CI720300.1|CI720300
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88904545|gb|CI711844.1|CI711844
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|2427972|gb|C72435.1|C72435
EST:     AGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: AGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88594346|gb|CI714304.1|CI714304
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88667495|gb|CI722234.1|CI722234
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88959424|gb|CI716793.1|CI716793
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88674644|gb|CI728757.1|CI728757
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88673162|gb|CI727276.1|CI727276
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88417331|gb|CI578992.1|CI578992
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|33681239|gb|CF309478.1|CF309478
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88693111|gb|CI736686.1|CI736686
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88595180|gb|CI715336.1|CI715336
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
EST: gi|88410825|gb|CI578631.1|CI578631
EST:     CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAG                         TTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC
genomic: CCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTC

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: 14 (upstream exon), 62 (downstream exon)
Score: 2

ATTATCTACTTCCTCTACCTCCCCTAATCCACTCCACTCCACCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaactt ... ttggctgcagTTGTTGCAGCAAGGAGGCATGGCGGTGGGGGGTGAAGAAGAGAAGCCCTTCAACTTCCTCCAGATTCTGTGTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTATCTACTTCCTCTACCTCCCCTAATCCACTCCACTCCACCGCAGCTTCTCCCGCGGCGAGGCGGCTCATCCCATCTCCACAGCCGCAGgtgggaacttgccaacggggattctctccgaccgattcaccgggatttctcccgcggtcgccgctccacccatgttttttttttttttgggttcttgcttgtccgtccctgacgaatgttgcaatggtgtttcttggctgcag

- - - - - - - - - - - - - - - - - - - - -  GCAGCT