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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttcttttcattccaatcagcactacgtctacacaaaatggatgtttcctttatgcttcctggtagactaagtatcctttttcccctcattttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGCT

Basic information

species Oryza sativa
transcript LOC_Os02g10180.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g10180.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 2
agtttcttttcattccaatcagcactacgtctacacaaaatggatgtttcctttatgcttcctggt--agactaagtatcctttttcccctcattt----tttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGCT
     |    |||||   || || | ||  |  | |    |   | | ||  |    |  |    |    | | |  || |  |||||  |  | |    |||||||||| ||||| || || ||  |||||||||||  || ||||| ||  |||||| |||| ||||| ||||||||  | ||||| ||||||||||||||| |
---ggccacccattc---tctgcccgactgcccctctgtctctctctctctctagcacagcacacttcgaatttaaaatgccatttccttttttctggaatttcagAAGGACAAGAAAAAGACCCTGCTACTTTGTTCGCACAAGCCTCAGGGATGATGGACCTGAGGAAGTATGATGGGGCGCTTGGCCTGCTAAATGCTGTGTT
















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|88360289|gb|CI612008.1|CI612008
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTACAAATGA
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|88421491|gb|CI618615.1|CI618615
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGC-AAGATAATGATCCATCTACTTTG
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTG
EST: gi|29664002|gb|CB660277.1|CB660277
EST:     CTTCGTCTTCGCTCACC                         ATTGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: CTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|88407064|gb|CI581151.1|CI581151
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAG
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAG
EST: gi|58679386|gb|CK068073.1|CK068073
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|88397149|gb|CI593361.1|CI593361
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|88731190|gb|CI754803.1|CI754803
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCT
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCT
EST: gi|88417075|gb|CI573790.1|CI573790
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGC-AAGATAATGATCCCTCTAC
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTAC
EST: gi|58664588|gb|CK053274.1|CK053274
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|88725664|gb|CI748923.1|CI748923
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTC
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTC
EST: gi|29685029|gb|CB681304.1|CB681304
EST:     CTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTATAAATGA
genomic: CTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|29663959|gb|CB660234.1|CB660234
EST:     CTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: CTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
EST: gi|58694698|gb|CK083385.1|CK083385
EST:     GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAG                         AAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA
genomic: GCCGCTGCTTCTCCTTCACTCCTCCCCCGTCTTCTTCGTCTTCGCTCAAGgtactgcgac ... attttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcctttatgcttcctggtagactaagtatcctttttcccctcattttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGCT
                             tatcctttttcccctc  CT-rich tract
                                           tcatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttcttttcattccaatcagcactacgtctacacaaaatggatgtttcctttatgcttcctggtagactaagtatcctttttcccctcattttttcagAAGGCCAAGATAATGATCCCTCTACTTTGTTCAAACGAGCCTTAGAAATGATGAACCTAAGGAAATATGATGGATCACTTGGTCTGCTAAATGCTGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG