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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtttttccatctatacaattagcgacagttgttaacaactattcatttattatagctaattattttttgacag

Basic information

species Oryza sativa
transcript LOC_Os02g11840.2
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 25
lower sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 25
TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtttttccatctatacaattagcgacagttgttaacaactattcatt-tattatagcta-attattttttgacag-----------
|  |||||||||| |||||||| |||| |||||||||||| |   | | || || || ||||||||||||| || | |||||  ||   |||   |        |  |  | | |   |  || || ||||| |  |   ||   |             
TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCA-AGTGGTTAAGTTTGTAAAGgtgaaatgctattccaagtaattaatactcatataccatagaacattttcagtcatactaaagctataacacaattaacccatcctattgtag
















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|88965746|gb|CI006623.1|CI006623
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTTCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|87021442|gb|CI274049.1|CI274049
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|29644063|gb|CB649070.1|CB649070
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|33800696|gb|CF326218.1|CF326218
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|25801672|gb|CA757633.1|CA757633
EST:     CGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTTTGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: CGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|87021165|gb|CI271972.1|CI271972
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86480883|gb|CI123516.1|CI123516
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86481559|gb|CI124192.1|CI124192
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86478917|gb|CI121550.1|CI121550
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88461084|gb|CI550247.1|CI550247
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86521390|gb|CI161596.1|CI161596
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|88267615|gb|CI379550.1|CI379550
EST:     ATAGTTAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATTTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
EST: gi|86886937|gb|CI324358.1|CI324358
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTTACTCCTACTGAAAGCTATGTGAAGGCCGTTTTCCTCCACTTGTA
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAA-CTATGTGAAGGCCGTTTTCCTCCACTTGTA
EST: gi|86477288|gb|CI119921.1|CI119921
EST:     ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG                         GTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT
genomic: ATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtt ... tttttgacagGTTGCTGACTCCTACTGAAACTATGTGAAGGCCGTTTTCCTCCACTTGTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAGgtgaagtgtttttccatctatacaattagcgacagttgttaacaactattcatttattatagctaattattttttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT