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

gtaacggatttatctacacttctttagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA

Basic information

species Oryza sativa
transcript LOC_Os02g57660.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
gtaacggatttatctacacttc---tttagctccaatcccatttcttgcgcagtgacaatcctt-------aacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
|||| | |||||  |   | ||   || |  |    |  | ||  ||  |   | ||  ||| |        | |  |||||| ||||||| || |||||||||||||| |||||||||||||| |||||||| ||||| ||||| |||||||||||||| || || |||||||| |||||||||||||
gtaatg-atttacatgagcatcaaattcatttaaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 5
----------------gtaacggatttatct-acacttctttagctccaat----cccatttcttgcgcagtgacaatcctt----aacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                | | |   || |  | |   |||||||| |  | |    ||| |   ||     || |  ||||||    || |  ||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| || || ||||| |||||||||||||| ||||| ||||||||||||||||| ||||
gtaactattgacatcagcaccaatttcacttgaggtttctttagtttaattttcccccttcctttttaatgtaatgatccttcttgaatatctgcaaattgcagTTTCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATCCACCGGAGGTTTGATTTGAAAGGATCATCTTTAGGCCGTTCTACTGATAAAA

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 5
------------------gtaacggattt-atctacacttctttagc--tcca-atcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                   ||||   ||| ||  | | |   |||    || | ||   ||     |   | |    ||   |||   ||  |  ||||||||||||||||| || ||||| || ||||| ||||| ||||| ||||| ||| |||||| ||||||||||||||||||  | || |||||| | ||||| |
ccaaaaaaaaaaaaagacttaacatctttcatgcaaaatgacttaataatctacattttatcaggaggctaatacttatatctaat-tttctattttgcagTTTCGCTTTGTCGTGATGGGAAATATGTTCTGCACAGAATTAAGGATCCATAGGAGATATGATTTGAAAGGTTCATCTCTTGGACGTTCTTCGGACAAGA

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 5
-----------------gtaac-ggatttatctacacttc----tttagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                  ||   | |  ||||   ||||     | ||  |   ||| ||||    |   | |    ||   |||   ||  |  ||||||||||||||||| |||||||| || ||||| ||||| ||||| ||||| ||| |||||| ||||||||||||||||||  | || |||||| | ||||| |
caaatgtaccacatcaaatatttgaacctatcatgacttaataatctaaattttatctcattaagaggctaatacttatatctaat-tttctattttgcagTTTCGCTTTGTCGTAATGGGAAATATGTTCTGCACAGAATTAAGGATCCATAGGAGATATGATTTGAAAGGTTCATCTCTTGGACGTTCTTCGGACAAGA

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
--------gtaacgga-tttatctacactt----ctttagctccaatcccatttctt---gcgcagtgacaatcctt-aacac----ttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
         ||   ||   ||||   ||||    ||| |  | ||    |||||| |          |  ||| ||| || |     ||     |||||||||||||||||||||||||| || ||||| ||||| || || ||||| |||||||| |||||||| |||||||| ||| | ||  | ||  | ||||| |
atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
------------gtaacggatttatctacacttcttt--agc-tccaatcccatttcttgcgcagtga--caatccttaacacttgc-----aaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
             || |  |   | | | ||| || |  ||| |   ||  ||| | | |  || |||   |||  ||   |  |       |  ||||||||||||||||| |||||||| |||||||| ||||| |||||  | || ||| |||||||||||||||||||||| |||||||| |||||| | |||||  
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatat-gtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ05102 (Selaginella moellendorffii), 3'ss of exon 4
gtaacggatttatctacacttctttagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                        ||| |   |     |   |||  ||  ||  |   | |||   |     || ||| | || || || || ||||||||||||||||||||||| |||||||| || ||  ||| |||||||||||| ||      ||| ||||  |||| | |  
-----------------------gtagttgtcagaaagtgatttg-acatggagcaatttcaacgtatttg--ttacagGTCCGGTTCGTAGTCATGGGTAACATGTTTTGCACGGACTTGAGGATACACCGCCGATATGATTTGAAAGGATCGCTTCAAGGACGTTGCACTGGCGAGG

upper sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ04955 (Selaginella moellendorffii), 3'ss of exon 4
gtaacggatttatctacacttctttagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                        ||| |   |     |   |||  ||  ||  |   | |||   |     || ||| | || || || || ||||| ||||||||||||||||| |||||||| || ||  ||| |||||||||||| ||      ||| ||||  |||| | |  
-----------------------gtagttgtcagaaagtgatttg-acatggagcaatttcaacgtatttg--ttacagGTCCGGTTCGTAGTCATGGGAAACATGTTTTGCACGGACTTGAGGATACACCGCCGATATGATTTGAAAGGATCGCTTCAAGGACGTTGCACTGGCGAGG

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|58666178|gb|CK054864.1|CK054864
EST:     TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAG                         TATCGCTTTGTTGTAATGGGTAACATGTT
genomic: TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAGgtaacggatt ... caaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTT
EST: gi|58608242|gb|CK036275.1|CK036275
EST:     TAACTAAGTTTTTTGGGCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAG                         TTTCGCTTTGTTGTAATGGGTAACATGTTT
genomic: TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAGgtaacggatt ... caaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTT
EST: gi|58660707|gb|CK049387.1|CK049387
EST:     TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAG                         TTTCGGGGGGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCAT
genomic: TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAGgtaacggatt ... caaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCAT
EST: gi|58688826|gb|CK077513.1|CK077513
EST:     TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAG                         TTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCAT
genomic: TAACTAAGTTTTTTGGCCTCCACAGGGTGAAGCCTTCTAGTGGTCAAAAGgtaacggatt ... caaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
                                 ccttaac  putative branch site (score: 3)
             atttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacggatttatctacacttctttagctccaatcccatttcttgcgcagtgacaatccttaacacttgcaaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT