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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA

Basic information

species Oryza sativa
transcript LOC_Os05g32110.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G071970_T01 (Zea mays), 3'ss of exon 5
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
              ||       |   ||||  || | ||| | | |  ||                || ||| |   |||||         |||||| ||||| |   | |  ||| ||||||||| || ||||||||||| || |||||||| || |||||||| |||||||| ||   |||||| ||||  || |||||||| ||||| || |||||
------------gtaagtaaacttgtcttatagaaaagaatagaaataaaccaac-----------ctacctcccaacctctc---------ctgatgtagtttgtctgtcccgtttcagATGATACGGCAATGTTCTGGGGTGTAAAGTTCTACAATGATTTGCTGATGCAAGCCGGCAAACTTGGGAATGTGCAATCAGAACTGCTTCTCCGCAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G06660.1 (Glycine max), 3'ss of exon 5
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
                    |  |   |   | |  || ||     |    | | |||| |  | | ||| | | |        |    |   |  |||  |   || ||| || |  ||||||||| || ||| | |||||| |||||||||| || ||||| |||||||||||||| || ||||| |||| ||| ||||| || ||  |  | |||||
----------------gtcataataactgcatgagcaacatattcttattttcgcaata-gaacatgtat-tttgtggaggcaccaaaatgattattgatctaagttacttttaat--agATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G27560.1 (Glycine max), 3'ss of exon 5
gtaagtcaatttacaaactgttctcctttat----ttaagaaaattggagtgcacttgtaatacgttcctttatctctctctc-----tctctctctttctctgat------gaagtttattcctt--------ctatttt----agATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
||||||    |  |||  ||||    ||| |    |||| ||  ||       |||   || | |||   |||  |||   |      | |  |||||  | | ||      |||| | ||| ||          |  |||    |||||||||||| ||| | |||||||||||||||||||| ||||| || |  |||||||| ||   ||| ||||  || ||||| || ||  | || |||||
gtaagtgcgatctcaacttgtttcagtttctggagttaaaaattttcttaaatactgtgaaaatgttatcttaattcttcataaaacattttactcttattttcataaacgagaaggtaattactgatcttaagttgcttttaacagATGATACTGCAATGCTGTGGGGAGTTAAGTTCTATAATGATTTTCTAAACCAAGCTGGCCCTAATGGCAATGTTCAATCAGAGCTACTCTTCCGAAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G04210.1 (Glycine max), 3'ss of exon 6
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
          | | |||||||      | |   |   |   |    | |||    ||||    | | ||| | | |        |    |   |  |||  |   || ||| ||    ||||||||| || ||| | ||||||||||||||||| || ||||| |||||||||||||| || ||||| |||| ||| |||||||| ||  |  | |||||
----------tcataaactgta-----tgagcaacatattcttattttcaccataaataa---catgtatttttgtagaggcgccaaaatgattattgatctaagttacttttaac--agATGATACAGCAATGCTTTGGGGAGTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAACTACTATTCAGAAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA18G50760.1 (Glycine max), 3'ss of exon 5
gtaagtcaatttacaaactgttctcctttat----ttaagaaaattggagtgcacttgtaatacgttcctttatctctctc--------------tctctctctctttctctgat--------gaagtttattccttctattt-------------tagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
|||||     |   ||  ||||    ||| |    |||| |   ||       |||   ||||  ||| |   |||   ||                | |   ||||  | ||||        |||| | ||| ||  | |||              |||||||||||| ||| | |||||||||||||||||||| ||||| ||||  |||||||| ||   ||| ||||  || ||||| || ||  | || |||||
gtaagcgtgatcctaacttgtttcgatttctggagttaaaagctttcttaaatactgtgaatattttcttaattcttcatcataaaacatcaaaacttttacttcttattttgataaactatagaaggtaattactgatttttaagttgcttttaacagATGATACTGCAATGCTATGGGGAGTTAAGTTCTATAATGATTTTCTCAACCAAGCTGGCCCTAATGGCAATGTTCAATCAGAGCTACTCTTCCGAAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G35400.1 (Glycine max), 3'ss of exon 5
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
                    |  |   |   | |  || |      |    | | |||| |  | | ||| | | |        |    |   |  |||  |   || ||| || |  ||||||||| || ||| | |||||| |||||||||| || ||||| |||||||||||||| || ||||| |||| ||| ||||| || ||  |  | |||||
----------------gtcataataactgcatgagcaacacattcttattttcgcaata-gaacatgtat-tttgtggagacaccaaaatgattattgatctaagttacttttaat--agATGATACAGCAATGCTTTGGGGACTTAAGTTCTACAATGATTTTCTCATGCAAGCTGGCCCTCTTGGTAATGTACAATCAGAGCTACTATTCAGAAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0083g01160.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtcaatttacaaactgttctc-ctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
                  | |  || ||||   | | |||||  |  ||      |  |  | |   | |  | |       |     |   | | |  |||||  ||  | | |    |||||||||||| ||| | ||||| ||||||||||| || ||| ||||| |||||||||| || |||||||||| ||||||||| || ||  | || |||||
-----------------atatcatcgctttgcatgacaaaatgtgcatgtttccctttt-tggtttatgacatattgaaaattgaacatgggtataac-aagttcttttttcccaac--agATGATACTGCCATGCTATGGGGGGTTAAGTTCTACAATGATCTGCTCGTGCAAGCTGGCCCTCTTGGAAATGTACAGTCAGAGCTACTCTTTCGGAAGGA

upper sequence: LOC_Os05g32110.3 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv17s0000g05070.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtca-atttacaaactgttctcctttatttaagaaa-attggagtgcacttgtaatacgttcctt-tatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
||| |||| || | |  |   ||    |||    |       |  |   ||  ||  ||||     | |  | || |   |||   ||      |||  ||||  | | |  |  |  |  |||||| ||||| ||||| |||||||| ||||| || || |||||||||   ||||||||||| ||||| ||||  |||||||| || ||  | || |||||
gtacgtcatatcttctcaagatttggttttgcaaagttgttgtctgccagctttttaaataaaaaacatgcaactgttcgtcttaatcctaacatcttgtgaatatgaattttggttatacagATGACACTGCCATGTTATGGGGAGTCAAGTTTTACAATGATTTGCTCTCTCAAGCTGGTCCTCTTGGGAATGTGCAGTCAGAGCTACTATTTCGAAAGGA

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|29629256|gb|CB634267.1|CB634267
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|58662260|gb|CK050940.1|CK050940
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|29629257|gb|CB634268.1|CB634268
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|58663803|gb|CK052489.1|CK052489
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|58686271|gb|CK074958.1|CK074958
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|58663197|gb|CK051883.1|CK051883
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|24208701|gb|AU225728.1|AU225728
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGAT
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGAT
EST: gi|3061251|gb|C91883.1|C91883
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|87018181|gb|CI297394.1|CI297394
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
EST: gi|29684532|gb|CB680807.1|CB680807
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATG
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATG
EST: gi|29657170|gb|CB653445.1|CB653445
EST:     GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAA                         ATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC
genomic: GCTGTTTAGCTTCAACTACAAGCCACTTACTCCATATGGAAGCAAGATAAgtaagtcaat ... tctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA
                         ctctgat  putative branch site (score: 4)
                                    tttattccttctattt  putative PPT
                                            ttctatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcaatttacaaactgttctcctttatttaagaaaattggagtgcacttgtaatacgttcctttatctctctctctctctctctttctctgatgaagtttattccttctattttagATGATACTGCGATGTTCTGGGGAGTTAAGTTCTATAACGATTTGCTCATGCAAGCTGGTCCACTTGGAAATGCACAGTCAGAACTTCTTCTGCGTAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG