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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaattattgttacatattttaaaaccaaattattgtgcatgtgagcatgttgttaaataaatattgacagtatt...

Basic information

species Oryza sativa
transcript LOC_Os03g08270.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08270.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G830874_T03 (Zea mays), 5'ss of exon 1
-----------------------------CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaatt--attgtt-acatattttaaaaccaaattat-tgtgca--tgtgagcat-gttgttaaataaatattgacagtatt
                             ||| ||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||||  |||  |   |||    ||| || || |  ||| || | | |||| ||||  | ||| | |||||   | |||| ||  ||| |   |||   ||||  |    
TTATGGTTTGAACTTGTTTGTGATAATAGCAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaacc--actgcaagatgctgaagtgaattattcaaacatttcaaaaaaatattgtatgtgctgttttgagtatcattgctctgtaac--ttgagtgc---

upper sequence: LOC_Os03g08270.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G017254_T02 (Zea mays), 5'ss of exon 5
CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaattattgttacatattttaaaaccaaattattgtgcatgtgagcatgttgttaaataaatattgacagtatt----
||||||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||||  | |||  | ||| |  |||| | |  |||  | | | |||| ||    ||||||||||   ||      |     | | |      | || |||      
CAAACACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgt--agatgaaccactgtgagataatgagctat--tcaaacatttcaagcaaaaattattgtatgtgctgtttttcgtatcactgctctgtaactgtaagtgaa

upper sequence: LOC_Os03g08270.3 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G830874_T04 (Zea mays), 5'ss of exon 3
CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaatt--attgtt-acatattttaaaaccaaattat-tgtgca--tgtgagcat-gttgttaaataaatattgacagtatt
||| ||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||||  |||  |   |||    ||| || || |  ||| || | | |||| ||||  | ||| | |||||   | |||| ||  ||| |   |||   ||||  |    
CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaacc--actgcaagatgctgaagtgaattattcaaacatttcaaaaaaatattgtatgtgctgttttgagtatcattgctctgtaac--ttgagtgc---

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|38470462|gb|CF954593.1|CF954593
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|86429806|gb|CI082229.1|CI082229
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|88845205|gb|CI084130.1|CI084130
EST:     CATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: CATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|4715235|gb|AU056352.1|AU056352
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|88847048|gb|CI001320.1|CI001320
EST:     AGGATAAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|38476095|gb|CF960228.1|CF960228
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|66921841|gb|CX108689.1|CX108689
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
EST: gi|86908615|gb|CI318954.1|CI318954
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCT-GAACAG                         GATAGGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAA
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATA-GGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAA
EST: gi|29615641|gb|CB620653.1|CB620653
EST:     AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAG                         GATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC
genomic: AGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgc ... cttttgacagGATAGGCAGGTTCTTTTAACTGGTGCCAATCCTTTAGCAAAGGAACTAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaattattgttacatattttaaaaccaaattattgtgcatgtgagcatgttgttaaataaatattgacagtatt

- - - - - - - - - -  AGGATG
- - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - AGCTCA