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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA

Basic information

species Oryza sativa
transcript LOC_Os02g40880.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G140116_T01 (Zea mays), 3'ss of exon 2
-ctattatgttatcgctgc-tcatttttctaatcggagttaattatattgtagtgctttgattattggatatcacataactctgtt---ttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
 |||  |   |||| |||| |    ||  | ||  |  ||  |   ||||   |   |  |  |||  |   | |||  |  ||||   |||||||||   |||||||||||||||||| ||||| ||||||||||||||| | ||||||||| |||| || || |||||||||||||||||||||||||||||||| |||||||
tctagcaacctatctctgcgttgccttgattatttgtcttgctgtaattg--attaatcaagcattcaagccctcatcgccttgttgcattctgtgaa---ccagGCACTTGTGGATGCCCCTGATATGGTCAGGTGCCAGGTGAACTTCAAGCGGCTCTCACTTACTGACATCAAGATTGACATCAAACGTGTCCCCAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G168330_T02 (Zea mays), 3'ss of exon 2
--ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
      ||| ||| |  |    |||| |  |  ||| |        ||||   || || |   |||  |   | |||  |  || |   |   |   |||||||||||||||| || ||||| ||||||||||||||||| ||||||||  |||| || || |||||||||||||||||||||||||| || || |||||| 
gttcgatat-ttaacaatatatatttgtggagccggtgcctcagtaattgatttggttaggc-attcaagcactcatggccttgatgcattctatggaccagGCACTTGTGGACGCCCCTGATATGGTCAGGTGCCAGATTAACTTCAAACGGCTCTCACTTACTGACATCAAGATTGACATCAAACGCGTTCCCAAGAAGT

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA03G06380.1 (Glycine max), 3'ss of exon 2
----ctattatgttatcgct---gctcatttttctaatcggagttaattata-----ttgta-gtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
    || |      | | |    | || |   | || ||  | |||   | |     ||| | |   | | |  ||| | | |  | |   |     | ||   ||| |  |||| ||||| ||||| ||||| ||||| |||| |||  |||| ||||| ||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||
gtaactctcccaccaccacccaagttcttacctttattcacatttacacacaaccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataat-attagGCTCTTGTCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G19890.1 (Glycine max), 3'ss of exon 2
-ctattatgttatcgctgctcatttttctaatcgg---agttaatt-atattgtagtgctttgattattggatatcacataactctgttttctgtga-atcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
 | | |  | ||     || ||  |    || | |   | |||||| | | |  ||  |  | | || |  | ||     ||    | |||     | |  |  |     | |   ||   ||||| ||||| |||| |||  |||| ||||| ||||||||||| || ||||| ||||||||||| ||  | ||||| |      
tcaaattagctaaatgagcccaaataataaaactgcctaattaattgacaattaagaccaatcagtaattaaaatggtgcaaaaagggtttagaaaatagAAGAAAATGATGGCACATCACCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTA------

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G32580.1 (Glycine max), 3'ss of exon 2
----ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcacataactctgttttctgtga-atcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
    |   |     | |     || |   | | |||  | ||||  |||      ||| |   || || ||  |        | |||| |   ||| |  |  |||||||||| ||||| ||||| ||||| |||| |||  |||| ||||| ||||||||||| || ||||||||||||||||||||  | ||||| |||||||
gtaacccctccaccacccaatttcttacctttgatcacatttaagcatacccatttgcatgttttcttagaagtagttgttttttgttgttgatgataataatagGCACTTGTCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTTACCGACATCAAGATTGACATCAAGAGGGTCCCTAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G35000.1 (Glycine max), 3'ss of exon 2
-----------ctattatgttatcgctgctcatttttctaatcggagttaattatattgta-gtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
           | |  |    |   ||   | || |||  ||    |   |     ||| | ||  | | |  ||| | | |  | |   |     | ||   ||| |  |||| ||||| ||||| ||||| ||||| |||| |||  |||| ||||| ||||||||||| || || || ||||||||||| ||  | ||||| |||||||
gtaactccccaccaccacccaagttcttacctttattcacatttacgcacacccatttgcatgttttcttagaattagttcttgctttgttgataatcctaataat-attagGCTCTTGTCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGATATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G00680.1 (Glycine max), 3'ss of exon 2
ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattgga---tatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
      |||   |  |  | ||   |   ||  |  ||    |  || | |   ||||||      |   | |  ||||| | | | | |  |   |   ||||| ||||| ||||||||||||||||| |||| |||  | |||||||||||||| || || |||||||||||||| || || ||  |  |||| |||||||
--gaggtgtccacattattgataagttggatgtgctttttacagcttttgggtatttgatgtcaaaaccatgtagcataatttt-tctaccatttgttgacagGCTCTTGTTGATGCTCCTGACATGGTGAGGTCCCAAGTGAACTTCAAGAGGCTATCACTCACTGACATCAAGATCGATATTAAGAGGATCCCCAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G00680.1 (Glycine max), 3'ss of exon 2
ctattatgttatcgctgctcatttttctaatcggagt-taattatattgtagtgctttgattattgga---tatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
      |||   |  |  | ||   |   ||  |  | | |     ||  |||  |||||||     |   | |  ||||| | | | | |  |   |   ||||| ||||| |||||||| |||||||| |||| |||  | |||||||||||||| || || ||||||||||||||||| || ||  |  | || |||||||
--gaggtgtagacattattgataagttgcatgtgcatgttacagctttcgagta-tttgatttcaaaaccatgtagcataatttt-tctaccatttgttgacagGCTCTTGTTGATGCTCCCGACATGGTGAGGTCCCAAGTGAACTTCAAGAGGCTCTCGCTCACTGACATCAAGATTGATATTAAGAGGATTCCCAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G08910.1 (Glycine max), 3'ss of exon 2
----ctattatgttatcgct---gctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcaca-taactctgtt-----ttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
    ||        | | |    | || |   | || ||  | |||   | ||     ||| |   || || ||  |     |  || ||||     | ||   ||| |  |||| ||| | ||||| ||||| ||||| |||| |||  |||| ||||| ||||||||||| || ||||| ||||||||||| ||  | ||||| |||||||
gtaactcccccaccaccacccaagttcttacctttattcacatttacacacatccatttgcatgctttcttagaattagttcttgctttgttgataatcctaataat-attagGCTCTTATCGATGCCCCTGATATGGTGAGGTCCCAAGTCAATTTCAAAAGGCTTTCCCTAACCGACATTAAGATTGACATTAAGAGGGTCCCTAAGAAGA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv11s0118g00670.t01 (Vitis vinifera), 3'ss of exon 3
-ctattatgttatcgctgctcatttttctaatcggagt-taattatattgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
 |||  |   |        ||| | ||  |     | | |  ||   ||   | |    ||| |||    ||| || |   |  ||   | |   |   ||||| ||||||||||| || |||||||| || ||||| || ||||| ||||||||||| || ||||| ||||| |||||||||||| | || || ||||| |
tctacaagcattgaatacatcaatattaaagatatactgttgtttccttcatgagaagagatgattatcaatctcagagtgcaattg--tatccctttgcagGCTCTTGTGGATGCACCCGACATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACTGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

upper sequence: LOC_Os02g40880.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv05s0049g01310.t01 (Vitis vinifera), 3'ss of exon 3
ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattg----gatatcacataactctgttttctgtgaatcacc----agGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
        || ||     | ||   |  | |  ||   |  |||| ||  ||| |||  ||| ||    || || |   |   | |  | |  |     |||    |||| |||||||| || ||||| ||||| || ||||| || ||||| ||||||||||| || || || ||||| |||||||||||| | || || ||||| |
-------attttcaaaattgataaatggattttgaaagatgtatactg-ggtgttttctttaatgtaaagagattatcaattacagagtgcaattggataccttgcagGCCCTTGTGGACGCACCTGATATGGTGAGATGCCAAATGAACTTTAAGAGGCTTTCACTCACAGATATCAAAATTGACATCAAAAGGGTGCCTAAGAAAA

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|86599617|gb|CI253602.1|CI253602
EST:     AGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACCGG                         GCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGG
genomic: AGGACTACGGCCGCCTCGTCGTCATCGTTGATGTCGTCGACCAGAACCGGgtaagcatcg ... gaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA
                          acataac  putative branch site (score: 3)
         tttgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattatgttatcgctgctcatttttctaatcggagttaattatattgtagtgctttgattattggatatcacataactctgttttctgtgaatcaccagGCACTTGTGGATGCTCCTGACATGGTCAGGTGCCAGATCAACTTCAAGAGGCTTTCCCTGACTGACATCAAGATTGACATCAAACGTGTCCCGAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG