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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g07560.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G082099_T01 (Zea mays), 3'ss of exon 4
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  ||| ||||  | | || |||  |   ||     |||  ||| |    |||  |     ||   |      |  | || |||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||  | ||||  |||||| ||||||||||||||||||||||  
gtaggtttcaatacacatgttgactcaacattatggtattc--ttctggaacgcctgtcagcctgcaac-----aatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGTCTACTTCTCCGGAGATGCTTTGTTGTTATTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G017204_T02 (Zea mays), 3'ss of exon 3
gtatattttaatatgcctattaacttcatgatac-caacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG---------------------------------------------------------------------------------------------------
|||  |||| ||| | ||   ||| | ||| ||  |  ||  |   |   | ||||      ||||||             || |||| |||||||||||||||||||||||||||||||||||||||||  |||||||||||||  | ||||  |||||| ||||||||||||| ||| ||||                                                                                                     
gtaggttttgatacgact--caacattatggtattcttctggaacgcctgtcagcctgcaacaatgtt-------------tgtagggagataccaagagtttccttgtttgcaagaagaaaatggctacaactccggagatgctttgttgttattgtccaactccattcaaacaattttttgagATTGTCACAAATATGAAATTTGACGAAGAGCCAAATTATGCCAAGCTTATCTCTCTTTTTGATGGTTTGATTGAAGCGCCTGCTTCGAGACAAATCGGAA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G110085_T01 (Zea mays), 3'ss of exon 5
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  ||| ||||  | | || |||  |   ||     |||  ||| |    |||  |     ||   |      |  | || |||| |||||||||||||||||||||||||||||||||||||||||||||||| |||||||  | ||||  |||||| ||||||||||||||||||||||  
gtaggtttcaatacacatgttgactcaacattatggtattc--ttctggaacgcctgtcagcctgcaac-----aatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGAAGATGCTTTGTTGTTATTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G508368_T01 (Zea mays), 3'ss of exon 3
gtatattttaatatgcctattaacttcatgatac-caacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  |||||||| | |    ||| | ||| ||  |  ||  |   |   | ||||      ||||||             || |||| |||||||||||||||||||||||||||||||||||||||||  || ||||||||||    ||||  ||| || |||||||||||||||||||| |  
gtaggttttaatacgacc--caacattatggtattcttctagaacgcctgtcagcctgcaacaatgtt-------------tgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACAACTTCGGAGATGCTTTATTGTTATTGTACAGCTCCATTCAAACAGTTTCTTAAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 10
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  ||| ||||  | | || |||  |   ||     |||  ||| |    |||  |     ||   |      |  | || |||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||  | ||||  |||||| ||||||||||||||||||||||  
gtaggtttcaatacacatgttgactcaacattatggtattc--ttctggaacgcctgtcagcctgcaac-----aatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTTTGTTGTTATTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G017204_T01 (Zea mays), 3'ss of exon 2
gtatattttaatatgcctattaacttcatgatac-caacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  |||| ||| | ||   ||| | ||| ||  |  ||  |   |   | ||||      ||||||             || |||| |||||||||||||||||||||||||||||||||||||||||  |||||||||||||  | ||||  |||||| ||||||||||||| ||| ||||  
gtaggttttgatacgact--caacattatggtattcttctggaacgcctgtcagcctgcaacaatgtt-------------tgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACAACTCCGGAGATGCTTTGTTGTTATTGTCCAACTCCATTCAAACAATTTTTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G458035_T01 (Zea mays), 3'ss of exon 8
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  ||| ||||  | | || |||  |   ||     |||  ||| |    |||  |     ||   |      |  | || |||| |||||||||||||||||||||||||||||||||||| ||||||||| |||||||||  | ||||  |||||| ||||||||||||||||||||||  
gtaggtttcaatacacatgttgactcaacattatggtattc--ttctggaacgcctgtcagcctgcaac-----aatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGTCTACTTCTCTGGAGATGCTTTGTTGTTATTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G164265_T02 (Zea mays), 3'ss of exon 10
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
|||  ||||||||  | | |  |||  | | ||     |||  ||  |    ||  ||   |   |    |    |  | || |||| ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||  | |||||||||||| ||||||||||||||||||||||  
gtaggttttaatacacatgtcgactcaacgttatggttttc--ttttggagcgcatatgtcagcct---gtaacgatgtttgtagGGAGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCAGAGATGCTTTGTTGTTTCTGTCCAGCTCCATTCAAACAGTTTCTTGAGA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 10
-----------------------------------gtatattttaatatgcctattaac--ttcatgatacc----aacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
                                    | | |||||| | |  |  ||    ||| || | |     || ||   || |   |  | | ||||    |   |||   |  | | |||||||| |  || ||||| |||||||| |||||||||||||| ||||| |||||| || |  |||| ||   |||  ||||||| || |||||||||||||
gtatttttgtagcatcttgttttatattgattccttttttttttaacaggttttatagtgattcttgcttcttagaaattttttttta---tgacaatttctcccttcttttggccatatctacagGGTGACAATAAAAGTTTTCTTGTTTGTAAGAAGAAAATGGCCACTTCCCCGGAGTTGATGTGCTGCTTTGTTCCTGCTCCATTTAAGCAGTTTCTTGAAG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 10
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgctt---aattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
||   |||  || ||  | |    || ||     ||   | ||   |  | | |  ||| || | ||   |  ||   |||  | ||||| || | |||||||||||||||||| ||||| || ||||||||||| || ||| || |  | || || |||||  |||||||||||||||| |||||||
gtgagtttatat-tgtttgtgtctttgatccattcaggctgaggaaacttcatctgattttagttttttctcatttggaatattacagGGAGACAACAAGAGTTTCCTTGTTTGTAAGAAAAAGATGGCTACTTCACCAGAGTTGATGTGTTGCTTTTGTCCTGCTCCATTCAAACAGTTCCTTGAAG

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S208_44V6.1 (Physcomitrella patens), 3'ss of exon 8
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAA---GAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
     ||||  | ||   |  ||    |||  | |  || | |    | |  ||   ||||        ||| ||  |||  |||     |   |   | |  |   | || |    || ||| |     ||     |      | |   || ||    |||| ||    ||  | |   |  ||   
----gttttcttgtgtggaagaagaaaatggcaacttctcctgaaatgctgtgctgtttctgcccggttttgttt--ttaaacagACGTTTTGGAGATGGTCACAAATATGAAGTTCGATGAAGAGCCAAACCAGAGCAAGCTCGTTCTACTCTTCGATTCCATCTTGGATCCTA-ATCCTACTGT--

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 7
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
                                  ||   |   || | |||      || |  | || | ||     || |  |||| || |  ||  | || || || ||||| ||||||||||| || || ||||||||| |  |||||||||| || ||||||||||| |||||| | ||| 
--------------------------------gtcaggctgttttaatattttagttttattgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACGTCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA

upper sequence: LOC_Os07g07560.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 7
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattcta-atgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
                                  ||   |  |||   ||     | || ||  | || | ||     || |  |||| || |  ||  | || || || ||||| ||||||||||| || || ||||||||| |  |||||||||| || ||||||||||| |||||| | ||| 
--------------------------------gtcaggct--gttttaatatattagttttatgttttacatgggcgcttttatagGGAGACAATAAAGGATTTCTGGTCTGCAAAAAGAAAATGGCCACATCCCCGGAGATGTTGTGCTGTTTCTGCCCGCCTCCATTCAAGCAGTTTTTGGAAA

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|58659496|gb|CK048176.1|CK048176
EST:     ACACCCTTATATTTCTAATAAGAGGAAGATTGCCTTGGCAAGGTTACCAN                         GGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCG
genomic: ACACCCTTATATTTCTAATAAGAGGAAGATTGCCTTGGCAAGGTTACCAGgtatatttta ... aattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCG
EST: gi|58656539|gb|CK045219.1|CK045219
EST:     GGAAGATTGCCTTGGCAAGGTTACCA-                         GGTGATACCAAGAGTTTCCTTGTTTGCAAGGAGGAAAATGGCTACTTCTCC
genomic: GGAAGATTGCCTTGGCAAGGTTACCAGgtatatttta ... aattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAA-GAAGAAAATGGCTACTTCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG
                                           ttaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatattttaatatgcctattaacttcatgataccaacttcagttcagattagccaattctaatgttgcttgcttaattatgcagGGTGATACCAAGAGTTTCCTTGTTTGCAAGAAGAAAATGGCTACTTCTCCGGAGATGCTAAGCTGTTTCTGTCCACCTCCATTCAAACAGTTTCTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG