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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG

Basic information

species Oryza sativa
transcript LOC_Os11g33240.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 12
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
||||| |    |||||||||||||  |||| ||| | ||||||  ||  ||| | |||    | |  | |      |  ||||||| ||||||| |||||||||||||| || |||||||||||||||||||| ||||||
gtaattttgcatccatccttgtttgtacttttat-tatgtttcagaagtactcgtttt--cctctcatactgtgacctgtcacctgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 13
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
||||| |    ||||||| |||||  | || | | | ||| ||  ||  |||||      ||  ||| |||||||||  | || || ||||||| |||||||||||||| || |||||||||||||||||||| ||||||
gtaattttgcatccatccctgtttctatttttgt-tatgtctcggaagtacttg------ttgttttcccctcatactgtgacttgtgttcttctagTGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063909_T03 (Zea mays), 3'ss of exon 11
---gtaatgtattc-catccttgttttgacttatatatttgtttct-taaagacttggtttgatttatttt---ccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
     |||  |  |  |   |||  |  |  | ||| | | ||| | | | |  ||||    | || ||||   |||||||||  | ||||| ||| ||| |||||||||||||| || ||| ||||| |||||||||| ||||||
gtaacaattcacgcgtacttttgcatccatctctatttctatttttgttatgttttggaagtacttgttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G063909_T01 (Zea mays), 3'ss of exon 11
gtaatgtat--tccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
||| | |    ||||||  | |||  | || | | | |||||   ||  |||||       || ||| |||||||||  | ||||| ||| ||| |||||||||||||| || ||| ||||| |||||||||| ||||||
gtacttttgcatccatctctatttctatttttgt-tatgttttggaagtacttg-------ttttttcccctcatactgtgacctgtgttgttctagTGATCATGAAGGCGGGAATATCAGTTCTCATACTGGTCATCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------------------------------gtaatg-tattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttct--tccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
                                                                       ||||| |  ||   | || ||||  |   | |       | |  |   | || |     || ||||  | | |  ||    |||| ||||  |  ||||||||||||||||||||||| ||||||||  |||| || |||
gttagtcctggttctcttcgtttcaacatgtctcattaattagaatacataagctaaagttttcttgtatataatgatgatcttcctttattttaccaactcttaccaaatttctatagcatgatcaaggtttttttttcccttgtcta---ctggtttctgttttagTGATCATGAAGGTGGAAATGTTAGTGCTCACGCTGGTCACCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------------gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttga--tttattttccctcataccttcacctgggttctt---ccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
                                      |||    |  ||  |  | |  | || | | ||   || ||||    ||   | ||  ||| | |  | |  | | ||        || ||   | ||||||||||||||||||||||| |||||||| ||||| || |||
gtctgtattaattttcgtcacccatgcatgtctccttaaataagcttaattatcttgtaaatttgtttgttc--tttttaagactttaaatagacctttgtataacattttgcttttctactattttttgctctagTGATCATGAAGGTGGAAATGTTAGTGCTCACACTGGTCACCTG

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 12
----gta-atgtattccatcct-tgttttgacttatatatttg--tttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
    ||  || | |  |||| | ||       | |||| |  |  |||||||  |  |   | | |      |   || ||   ||         | |||||||||||||||||| || |||||||||||||| ||||| ||||| 
gtgggtgtatatttctcatcttatggcaatgataatatgtaggattttcttattggatca-tataacaatcatatgcttattaatttttaaaatgtgttccagTGATCATGAAGGCGGGAATGTCAGTGCTCACACTGGTCATCTA

upper sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 12
lower sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
              | || |  |  |   || ||||   | ||||  || || ||  |  ||||  ||| | | | | || || | |  |  |     ||||   |||||||||||| ||||| ||||| |||||||||||||  ||||||
atctcattattaaatgatctgctgaacgttttttttttttaatatcatttttact--actactt--tttaaatgaatctcactgacagatgtat----gttcaaacagTGATCATGAGGGTGGCAATGTAAGTGCTCATACTGTGCATCTG

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|3758954|gb|C96653.1|C96653
EST:     GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACAC                         TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
genomic: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACACgtaatgtatt ... gttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
EST: gi|38470398|gb|CF954529.1|CF954529
EST:     GATGATCCCAAAATGCTCGAGTTGATGCGACTATATATGACAATCCACAC                         TGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
genomic: GATGATCCCAAAATGCTCGAGTTGATGCGACTATATGTGACAATCCACACgtaatgtatt ... gttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG
            gtttgat  putative branch site (score: 5)
                                              ttcttcc  putative PPT
             tttgatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtattccatccttgttttgacttatatatttgtttcttaaagacttggtttgatttattttccctcataccttcacctgggttcttccagTGATCATGAAGGTGGAAATGTCAGTGCTCATACTGGACATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA