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

gtaaactacgcgcaccaccataaattgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG

Basic information

species Oryza sativa
transcript LOC_Os05g24550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g24550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G108849_T04 (Zea mays), 3'ss of exon 5
-----------------gtaaactacgcgcaccaccataaattgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG
                 ||||  |   |   | | |||| ||| ||| | ||   | |       |||||| ||       |||| ||||||||  |||  |  |||||||||||||||||| |||||||| ||||||||||||||||| |||||||| ||||| ||||||||  ||||||||
cttcatgagcagatcaagtaagttcaacagtctagcatatattattagtgcctaaaaga---gcgatgcaacatgcttgtagtataatgtcttgtctgatgacAACAGGGTCACTGTGGCTCTTGTTGGGCTTTTGGTGCTGTGGAGTGCCTCCAGGACCGTTTTTGCATTCACCTCAACATG

upper sequence: LOC_Os05g24550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA03G38520.1 (Glycine max), 3'ss of exon 5
gtaaactacgcgcaccaccataa----attgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatga--cagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG
|| | |  |         || |     ||  ||||   |||      ||| ||   |   | ||   | |  |   || | || |   ||||  |||||||||||||| || |||||||||||||||||||| || |   |    ||||| || |||||||||||  |  | 
gtgatcctcatattttctcacactgacatctttaaatacattcaatgttaaaa--gagtttctagctgatccttcatccttgt-gctgatgattcagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTT

upper sequence: LOC_Os05g24550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G41120.1 (Glycine max), 3'ss of exon 5
gtaaactacgcgcaccaccataa----attgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG
|||| |  |         || |     ||  ||||   |||     |  ||  |  ||||  |   || |   ||   |  | |||  ||  |||||||||||||| || |||||||||||||||||||| || |   |    ||||| || |||||||||||  |  | 
gtaatcctcatattttctcacactaacatctttaaatacattcaattcaaggttcaaagagttttcagctg--atccttgtgctgatgatt-cagGGTCACTGTGGTTCTTGTTGGGCATTTGGTGCTGTTGAATCATTGTCAGATCGCTTTTGCATTCATTTTGATGTA

upper sequence: LOC_Os05g24550.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0005g02820.t01 (Vitis vinifera), 3'ss of exon 4
----------gtaaactacgcgcaccaccataaattgttaatcccatgagggttt---agaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG
           |  | |      | |    |   |   |||    ||||||  ||   ||||     | | || |   |  | | | ||  ||    |   |||||||| |||||||| |||||||| ||||||||||| || |  ||    |||||||| || || |||||   ||||
gtaacttggtttgcattttatttagcgttgtccctatataaatgaatgaggaattctcagaaatttgggtttatttatttatttatttttattttttaaatcagGGTCATTGTGGCTCTTGTTGGGCTTTTGGTGCTGTTGAATCGCTGTCAGATCGTTTTTGTATCCATTTTGGCATG

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|58688070|gb|CK076757.1|CK076757
EST:     TTGGGACCATACTTGATCAG
genomic: TTGGGACCATACTTGATCAG
EST: gi|29666315|gb|CB662590.1|CB662590
EST:     TGGGGACCATACTTGATCAG
genomic: TTGGGACCATACTTGATCAG
EST: gi|29680417|gb|CB676692.1|CB676692
EST:     TTGGGACCATACTTGATCAG
genomic: TTGGGACCATACTTGATCAG
EST: gi|58609130|gb|CK037163.1|CK037163
EST:     TTGGGACCATACTTGATCAG
genomic: TTGGGACCATACTTGATCAG
EST: gi|29656753|gb|CB653028.1|CB653028
EST:     TTGGGACCATACTTGATCAG
genomic: TTGGGACCATACTTGATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagggtttagaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG
                                        ggttgac  putative branch site (score: 4)
                   atataataggtattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactacgcgcaccaccataaattgttaatcccatgagggtttagaatgcaagatataataggtattatgtcttggttgacaatgacagGGTCACTGTGGCTCGTGTTGGGCATTTGGTGCTGTGGAGTGTCTCCAGGATCGTTTCTGCATTCATTTCAACATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG