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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag

Basic information

species Oryza sativa
transcript LOC_Os02g49980.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 3
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag
||||||||||||||| || |||||||||||||| |||||  |||||||||||||||| || || || || ||||| ||||||||||| |||| || ||  || ||| |  |   |||||||  |    |  ||  |  || || |||| | | ||||   |||||| |||
CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaa-cttaagatgcattaccatgcttgattggtgttt--tgattctaatccatggctgctgtgcttcgcag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G089454_T01 (Zea mays), 5'ss of exon 2
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag
||||||||| ||||| || ||||| ||||||||||||||  |||||||||||||||| ||||| || || ||||||||||||||||| |||| || |       |  |  ||  ||||||| ||| | |  ||  |  || ||||||||| | |||    |||||  |||
CTTGTTTTTTAAGCAAGAAATGGAACTCTCCCTGGTTGGGTTGCAGAATGCTGGGAAGACATCGCTGGTCAATGCTGTTGCTgtatgcatcaactcag------tcaagatacattaccatgtta-tctggtgttt--tgattttaattcatggcttctgtgctttgcag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G41170.1 (Glycine max), 5'ss of exon 2
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacg--gaatctttatttatcttaccattttaatgttatgcctggtggttttaat----tcgttgctggcat-gcttctcag----------------
||||||||| || ||||||||||| || || || |||||||| ||||||||||| || || || || || |||||  |||||||  ||  |  ||   |  |  |    |||| |    | ||||  |     ||       ||| || |      |||  || ||| | |  |  |                
CTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCTgtgagttgctgctgctgctgcgttgcaattttttactcaatttagaaaccctgaagttcagttctagtataactgttattgacattggtatttggttttgtttacctgcag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA14G39540.1 (Glycine max), 5'ss of exon 2
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatc--taacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag--------------------------------------------------
||||||||| || ||||||||||| || || || |||||||| ||||||||||| || || || || || |||||  |||||||  ||  |  |   |  | ||| || | | |  |||  | || ||   |     |     |||   ||  || |||  ||   |||||                                                   
CTTGTTTTTTAAACAGGAGATGGAACTTTCACTTGTTGGCCTTCAGAATGCTGGCAAGACTTCTCTTGTCAATGCAATTGCTgtgagttgctgcagcattgcaattttgactcaatttagaaattaaaccctgaaatt--caatttctgtt-attactgttattgctctcatggccttgttttgacattacattgatgtttggtttttttgtttacctgcag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 5'ss of exon 2
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca--tctaacggaatctttatttatct--taccatttt-----aatgttatgcctggtggttttaattc--gttgctggcatgcttctcag-
|||||||||||| || ||||||||||| || || ||||| || || ||||||||||| || || || || |||||  |||||||  |||  |  |  | | ||   |||| |       ||  ||| |     ||   ||  | |    |||| | |||  |||          || |||  
CTTGTTTTTCAAACAAGAGATGGAGCTGTCACTCGTTGGACTTCAAAATGCTGGGAAGACTTCTCTTGTCAATGCCATTGCTgtgagtagaaatttcatcagaggttttagtcgataaatagtattctcgaacaaatctaatcttacgcgtttcacttcttgttttctttggatttgtcaag

upper sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 5'ss of exon 3
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccatttta-atgt-tatgcctggtggttttaattcgttg-ctggcatgctt--ctcag----------
| |||| |||||||| ||||||||||| || ||| | || |||||||| |||||||||||||| || || |||| | |||| ||||||||| | |||     || |     | |   | ||     |||  |||    | ||  |  || | || | | | || | |    || |          
CCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatc-tgtaattttctcctccgcaagcaagctatggcgcatgcctataaacgctg--tacaagttgtggaccgtcagggtcagttcggattatttaca

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|8324374|gb|AU091530.1|AU091530
EST:     CTGGGAAAACATCCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: CTGGGAAAACAT-CACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|33817712|gb|CF334689.1|CF334689
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|88434251|gb|CI589316.1|CI589316
EST:     GGCTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: GG-TTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|88342916|gb|CI640249.1|CI640249
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|88575977|gb|CI670122.1|CI670122
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCCACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|33808162|gb|CF329970.1|CF329970
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|88345402|gb|CI656060.1|CI656060
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|86600191|gb|CI251561.1|CI251561
EST:     GAATGCTGGG-AAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: GAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|55442549|gb|CV734564.1|CV734564
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|66923097|gb|CX109945.1|CX109945
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|58665641|gb|CK054327.1|CK054327
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTTGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|88347247|gb|CI632532.1|CI632532
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|33818441|gb|CF335055.1|CF335055
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|58586064|gb|CF984372.1|CF984372
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTTGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT
EST: gi|55414064|gb|CV726440.1|CV726440
EST:     TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCT                         ACAGGTGGCTACAGCGAAGACATGATTCCAACT
genomic: TGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatca ... tgcttctcagACAGGTGGCTACAGCGAAGACATGATTCCAACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag

- - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT