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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG

Basic information

species Oryza sativa
transcript LOC_Os02g56540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G408308_T01 (Zea mays), 3'ss of exon 3
gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
|||||  | |  ||||    |||||  | ||||||   |         ||        || | |  |||    |    || | |||    |||||||||||||| ||||||||||||||||||||| |||||||||| ||||| ||||||||| |||||||| ||||||||||||||||||| ||||| |||||||
gtacactactacaaaaaagtacatttattgatacagcctctcctccctaa--------tgatgatctaaatatt----tccttcattgcatttcagGATTCATTCGAGGATGACAAATCAAAAATCCTGATGATTCTGTGTGCTAGTCCTGACGCAAAGGAACTGCACAAGACAGTTTCTACTTTGGAATATGGTG

upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G062084_T01 (Zea mays), 3'ss of exon 4
gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
|||||  | |  |||| |  |||||  | |||||||   | | ||       |  |||  | | |  |||   |     | |  ||    |||||||||||||| ||||||||||||||||||||| | |||||||| ||||| |||||||||||||||||| ||||||||||||||||||| || || |||||||
gtacactactacaaaaatctacatttgttgatacaa-cctctcct------ctctagcgacgatctaaatattt-----cctttattgtatttcagGATTCATTCGAGGATGACAAATCAAAAATCCTAATGATTCTGTGTGCTAGTCCTGACCCAAAGGAACTGCACAAGACAGTTTCTACTTTAGAATATGGTG

upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G150984_T02 (Zea mays), 3'ss of exon 4
gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
|||||  | |  ||||  | |||||  | |||||    |    |    ||           || |  |||   |     | | |||    |||||||||||||| ||||||||||||||||||||| |||||||||| ||||| |||||||||||||||||| ||||||||||||||||||| ||||| |||||||
gtacactactacaaaagattacatttattgatactgcctctcccccctaa-------tgattatctaaatattt-----ccttcattgcatttcagGATTCATTCGAGGATGACAAATCAAAAATCCTGATGATTCTGTGTGCTAGTCCTGACCCAAAGGAACTGCACAAGACAGTTTCTACTTTGGAATATGGTG

upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G029134_T01 (Zea mays), 3'ss of exon 3
gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
|||||  | |  ||||    |||||  | |||||||  |         ||        || | |  |||    |    || | |||    |||||||||||||| ||||| ||||||||||||||| |||||||||| ||||| |||||||||||||||||| ||||||||||| ||||||| ||||| |||||||
gtacactactacaaaaaagtacatttattgatacaacctctcctccctaa--------tgatgatctaaatatt----tccttcattgcatttcagGATTCATTCGAGGACGACAAATCAAAAATCCTGATGATTCTGTGTGCTAGTCCTGACCCAAAGGAACTGCACAAGACAATTTCTACTTTGGAATATGGTG

upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA10G32610.1 (Glycine max), 3'ss of exon 5
----gtacaagattctaaaatttcac--attcctcgatacaaatt-tatactgt--aaaattaaagctgctaacgtaatgcctacg-atcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
     ||  ||  | |  | ||      ||| ||  || ||  || |||  | |   || ||  |  || |      ||   |  | || |||| |   |||| ||||||||||||| ||||| || ||||||||  | ||||| || |||||||||||||| || |||||    ||||||||| | |||||| | || ||||| |
gtaaataatagtctttttagttgagtcaattgctgaattcatgttctatgttatttgaagttttatttgatgtgaatatttttttgtatattccct---ttttaagGATTCATTTGAAGATGATAAGTCAAAAATTCTAATGATACTGTGTGCAAGTCCTGATCCTAAGGAGACACACAAGACAATCTCTACACTTGAATATGGAG

upper sequence: LOC_Os02g56540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA20G34970.1 (Glycine max), 3'ss of exon 4
-------gtacaagattctaaaatttcacattcctcgatacaaatt---tatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
        |  |   || |||        ||| || ||| || |||   | |  | | || ||  |     |      |    | |    |||| |   |||| ||||||| ||||| ||||| || ||||||||  | ||||| || |||||||||||||| || |||||  | ||||||||| | |||||| | || ||||| |
gtaaatattgtagtcttttaattgagtgaattgctagattcatattctctgttatttgaagttttattgattgtgagtactttttctgctttccct---ttttaagGATTCCTTTGAAGATGATAAGTCAAAAATTCTAATGATACTATGTGCAAGTCCTGATCCTAAGGAGATACACAAGACAATCTCTACACTTGAATATGGGG

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|58599102|gb|CK009630.1|CK009630
EST:     GTGACTCCCATGTCCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAG                         GATTCATTTGAGGACGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGT
genomic: GTGACTCCCATGTTCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAGgtacaagatt ... gaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGT
EST: gi|58671945|gb|CK060631.1|CK060631
EST:     CTCCCATGTCCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAG                         GATTCATTTGAGTGACGACAAATCAAAAATCTTGATGATTCTCTGTGCAAG
genomic: CTCCCATGTTCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAGgtacaagatt ... gaattttcagGATTCATTTGAG-GATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAG
EST: gi|58606121|gb|CK034154.1|CK034154
EST:     GTGACTCCCATGTCCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAG                         GATTCATTTGAGGACGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGT
genomic: GTGACTCCCATGTTCCATTTCGAGACAGCAAGCTCACAATGCTCTTGCAGgtacaagatt ... gaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG
                 tgctaac  putative branch site (score: 1)
                                                ttttc  putative PPT
     taaaattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaagattctaaaatttcacattcctcgatacaaatttatactgtaaaattaaagctgctaacgtaatgcctacgatcttccatgaattttcagGATTCATTTGAGGATGACAAATCAAAAATCTTGATGATTCTCTGTGCAAGTCCTGACCCAAAGGAATTGCACAAGACAGTTTCTACATTGGAGTATGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG