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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc...

Basic information

species Oryza sativa
transcript LOC_Os11g29190.5
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G156673_T02 (Zea mays), 5'ss of exon 1
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggta-accccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaa--aattttacc--------------------------------------
                                         || ||||||| || |||||| |||||||  || |||||||||||||||| |||||||| ||||||||||| |||||| |||||||||| |||||||||||||| |  |    | |||         ||   || ||  |    || |       |||  |                                        
-----------------------------------------AGGTCATGGCTGTCCGCATCATCAAGCATACCCTGGAGATCATCCACCTGCTCACCGATGCCAACCCCATCCAGGTCGTCGTCGACGCGATCATCAACAGgtacagtcttaatctcggctaataaccgttaaacctactcgttactatatgttgattccattcagtatgctggatccccccctgaaccgtgtgtgtattt

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 2
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctcttt-----cgaaccagtaaaattttacc------------------------------------
                                         || |||||||||| |||||| | |||||| || |||||||||||||||| ||||| |||||||| ||||| |||||  |||| |||||||| |||||||||||   ||    |   |  | | | | ||| |||||| |     |   | | ||| |  | | |                                    
-----------------------------------------AGGTCATGGCCGTCCGCATCATGAAGCACACCCTGGAGATCATCCACCTGCTCACTGACGCCAATCCCATCCAGGTGGTCGTGGACGCCATTATCAACAGgtactaccttgctctcctgtcctcactcccgatctctgtattgtcaggctaataacagctaaacttgttactttatgctgatactttttggaatgcggta

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G26840.2 (Glycine max), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccag--taaaattttacc---------------------------------------
                                         || ||||||| ||  | ||  ||||||| |||||||||||||||||| | ||||| |||   ||||| ||||||||||| || || ||| ||||||| |||||    |   | | | |     ||           |   | |   |  |    |||||                                         
-----------------------------------------AGCTCATGGCTGTCAGGATTATCAAGCATGCCATGGAGATCATCCACTTGCTCACTGACCTGAACCCAATTCAGGTCATTGTTGATGCCGTCATCAATAGgtatgttcgggtgttgagaacttcttttttttgtgttgatggatttgctttgggttttaattgcagatgagttgtttgtgctggtgtcatcaattgtaga

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: AT3G11940.2 (Arabidopsis thaliana), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc--------------------------------
                                         |  | ||||| ||  | ||||||||||||||||||||||| ||||||||| |  | |||   ||||| |||||||||||| | ||||||||  ||||||||||  |   ||||  |   |  |||     | | || || |||| || || ||||||                                  
-----------------------------------------AATTGATGGCTGTCAGGATCGTCAAGCACGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCAATTCAGGTCATCATTGACGCCATTGTCAACAGgta--ctaaccttgtgaagtatgctgaaatagtatcattggaacaaggaacattttattcttattaatgttttgtttgttgcttgagccag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggta-accccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc--------------------------------------
                                         || | ||||| ||  | ||||||||||| ||||||||||| ||||||||| |  | |||   ||||| ||||| || ||| | || |||||  | |||||||| |       |      ||     |    ||  |||| ||  |  || |   |  ||                                       
-----------------------------------------AGTTGATGGCTGTCAGGATCGTCAAGCATGCCATGGAGATTATCCACCTCTTGTCTGACTTGAACCCGATTCAAGTTATCATTGATGCCATTGTTAACAGgtatattaagattgctatactgaaacctgtaaaattcttgcgtgcttgttactatgaactgaatctaattaagaaggtttgttctttatgtgaattag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP01658 (Chlamydomonas reinhardtii), 5'ss of exon 3
---GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc
   |  |||||| || ||||||||||||||||||||||| |||||| | ||||| ||| ||| | |    ||    | |          | |   |  | | |       | |  | ||  |  |  |  | || | |     ||| || |    |   |                                           
CCTGTGCAACTCCCTGATGATGCACGGCCGCAACAACGGCAAGAAGCTGATGGCGgtgagcagcat-ggtcaatggaggagcgcggcatagcgggttgcgggctgtggggcaa--cgggcgacgggtgtggacaccgtggg--ggtgacgcttggtgctg-------------------------------------------

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S101_208V6.1 (Physcomitrella patens), 5'ss of exon 2
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgc--tcgcccaatct-ctttcgaaccagtaaaattttacc--------------------------------------------------------------------------------------
                                         || | ||||| || |||||||| |||||||| |||||||| || ||||| || ||||||   ||||| || |||||||||||||||||||||||||||||||     | |     |  |   |   | || |      | || |||    |     | |                                                                                         
-----------------------------------------AGTTGATGGCTGTACGCATCGTGAAGCACGCGATGGAGATTATTCACCTACTGACCGACCAGAACCCTATCCAGGTCATCGTCGACGCCATCATCAACAGgtgggttctctcgaagttccatgaggtggcacgggagacgtttgaatgcttgggcgtgtgtgtgttgtgaagctgggaaaggtttttaggcattatttggtataatgccagggttttaaagtaagagggagtcatggtgtgagtgcag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S114_143V6.1 (Physcomitrella patens), 5'ss of exon 2
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc-----------------------------------------------------------------------------------------------
                                         || | ||||| ||||||||||| |||||||| ||||||||||||||||| || || |||   |||||||| ||||||||||| || |||||||||||||||||      | |    | |||   | ||   || |     | |   |       |   |                                                                                               
-----------------------------------------AGTTGATGGCGGTGCGCATCGTGAAGCACGCGATGGAGATCATCCACCTGCTGACGGACCAGAACCCCATCCAGGTCATCGTGGATGCCATCATCAACAGgtaggttatc-tcgaacacttgtttagctgcatattggggggagaggcgggggatgggcgcatgggcgggaggagaggttgcaacaggaatttagggttatgcgggatgatgtggggctcgggagctgagaggtcgcggtgggaatgggtacag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 2
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggt---aaccccccctttc-----gcgcttcgctcgcccaat---------ctctttcgaacc-agtaaaattttacc---------------------------------------------
                                         || | ||||| || ||||| || |||||||| ||||||||||| ||||| || || ||    |||||||| ||||||||||| || || |||||||||||||   || |    |||||     | | ||     |   |||         | || | ||  | |||  ||||  |                                               
-----------------------------------------AGTTGATGGCTGTCCGCATTGTGAAGCACGCTATGGAGATCATTCACCTTCTGACTGATCAGAACCCCATCCAGGTCATCGTTGATGCTATCATCAACAGgtttgaatcttatctttctattggtgtttgatgtggaaaatgaaatgcgacactcttgaggcgagtctaattcaattgtagcaatttttagtggcatgaggcatatcttttatctgctgcag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S10_385V6.1 (Physcomitrella patens), 5'ss of exon 2
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggt---aaccccccctttcgcgct-tcgctcgccca------atctctttcgaaccagtaaaattttacc----------------------------------------
                                         || | ||||| || ||||| || ||||||||||||||||| ||||| ||||| || |||   ||||||||||||||||||||||| || || ||||||||||    || |   |    | | | |||  |  ||       |    | |    |   | |||| ||  |                                        
-----------------------------------------AGTTGATGGCTGTCCGCATTGTGAAGCACGCCATGGAGATTATCCATCTCCTGACTGACCAGAACCCCATTCAGGTCATCGTCGATGCTATTATCAACAGgttcggacgcaatcccgtgtgatatcgaacatcctgaggacacaattctttttctgattaaatattgtcaatttgtctctgagcgacagtgttttcccatacattgcag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgct-tcgctcgcccaatctctttcgaaccagtaaaattttacc
                                         || | ||||| | |||||| || |||||||| ||||||||||| ||| | ||||| || || || || || ||  ||||||| ||||||||||||||||||||   |      || |  | |  |     || |   |||    ||       ||  |  
-----------------------------------------AGTTGATGGCTGGGCGCATTGTGAAGCACGCGATGGAGATCATTCACTTGCTCACAGATGCGAATCCGATCCAAATCATCGTGGACGCCATCATCAACAGgtagagctatagatctctttgttacaacttcattgatttttcgtccttcctgcttgcag-

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc------
                                         || | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||        |   | |    |    ||    |  ||| | |         |||  |       
-----------------------------------------AGCTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta-tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag

upper sequence: LOC_Os11g29190.5 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ37091 (Selaginella moellendorffii), 5'ss of exon 3
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc------
                                         || | ||||| |  ||||| || ||||| || ||||||||||| ||| | ||||| ||||||||||| || ||  | || ||||| || ||||||||||||||        |   | |    |    ||    |  ||| | |         |||  |       
-----------------------------------------AGTTGATGGCTGGTCGCATTGTGAAGCATGCAATGGAGATCATTCACTTGCTCACGGACGCCAACCCGATCCAAATTATTGTCGATGCTATCATCAACAGgta-tagaggttcaagtgagcaggattccaggacagttttggattttctctctttctctttgcag

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|86257628|gb|CI063981.1|CI063981
EST:     CCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGAC                         GCCAACCGTTGAGTGGTGATCCCATGTCATTGTGCTAAAGCTCTTGCGCTG
genomic: CCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaacccca ... tgttgccaagGCCAACCGTTGAGTGGTGATCCCATGTCATTGTGCTAAAGCTCTTGCGCTG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCAACTCGCTCATGATGCACGGCCGCAACAACGGGAAGAAGATCATGGCCGTGCGCATCGTCAAGCACGCCATGGAGATCATCCACCTCCTCACCGACgccaaccccattcaggtcatcgtcgacgccatcatcaacaggtaaccccccctttcgcgcttcgctcgcccaatctctttcgaaccagtaaaattttacc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgacgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcgccc