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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccacaaagttaaattgtgtttttatcaagatcaggacgacatctcaatagcaaataattaaccatatcattgtttctctcttgccggtatatgg...

Basic information

species Oryza sativa
transcript LOC_Os03g19510.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G121456_T03 (Zea mays), 5'ss of exon 8
GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccacaaagttaaattgtgtttt-tatcaagatcaggacgacatctcaatagcaaataattaaccatatcattgtttctc-tcttgccggtatatgg
| ||||||||||||||||| |||||||| |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||  | ||| ||     | ||     ||||| | |    |   ||   || || |   |||  ||  ||||  |   ||||| | |   |   | |  |
GAAAGCGATACAGCTTACCAAACTCAAGGATAATGATCCATCAACCTCTTGGAGGGGCCCAAGGACAGGAGACTGATCTTGAGATTCAGgtaaactcgcaatgtggggctatggaaagtatcatgctttctagaccagtacagtatct--taaccaaagatattctcagttctcgtttcttctcaacaaag

upper sequence: LOC_Os03g19510.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 5'ss of exon 8
GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccacaaagttaaattgtgtttttatca---agatcag--gacgacatctcaatagcaaataattaaccatatcattgtttctctcttgccggtatatgg
| ||  |||| ||||| || |||||||| || ||||||||||| |||||||| ||||| |||||     | |||||  | || || |||||   |        |     | |  ||  | ||      || |  ||  |||| |  || | |  | ||  |  | | ||       | |  || |  | |    
GAAAAAGATATAGCTTGCCAAACTCAAGGATCATGATCCATCAGCCTCTCGGTGGAGCTCAAGGTGGGCAAACTGACATAGATATTCAGgtgtgttgtttctctcttgctttcattccaccatttgtttctgtcgattacatgttgat-gtaccttatctaatacagcagatacattatgatgtctttgt----
















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|86254683|gb|CI060994.1|CI060994
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88969043|gb|CI099028.1|CI099028
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88994799|gb|CI036380.1|CI036380
EST:     ATCGACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|33682025|gb|CF310264.1|CF310264
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|86541399|gb|CI181605.1|CI181605
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|218500705|gb|FG952597.1|FG952597
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|44675627|gb|CR289061.1|CR289061
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88536630|gb|CI465289.1|CI465289
EST:     GAGACTGATCTTGAGATCCAG                         GCTTATGAGATGGTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: GAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|33682024|gb|CF310263.1|CF310263
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88538671|gb|CI467722.1|CI467722
EST:     ATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|86596355|gb|CI268655.1|CI268655
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|8858878|gb|AU096196.1|AU096196
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|29683121|gb|CB679396.1|CB679396
EST:     CTCTCGGAGGAGCCCTAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: CTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|33801418|gb|CF326580.1|CF326580
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88548588|gb|CI476400.1|CI476400
EST:     GACAAGAGACTGATCTTGAGATCCAG                         GGTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: GACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88832375|gb|CI019316.1|CI019316
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88547486|gb|CI477784.1|CI477784
EST:     CGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: CGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88531129|gb|CI459577.1|CI459577
EST:     GACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: GACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88544322|gb|CI473019.1|CI473019
EST:     CCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: CCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88227214|gb|CI228327.1|CI228327
EST:     GGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: GGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88991452|gb|CI034787.1|CI034787
EST:     CGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: CGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|89198430|gb|CI007490.1|CI007490
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|109711590|gb|CI013195.1|CI013195
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88546312|gb|CI475938.1|CI475938
EST:     GACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGGTAACCTGAATGGATACCTAGCATAC
genomic: GACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|88541729|gb|CI471017.1|CI471017
EST:     TCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGGTGACCTGAATGGATACGTAGCATAC
genomic: TCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|86423150|gb|CI060723.1|CI060723
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|58030704|gb|CX728247.1|CX728247
EST:     CTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: CTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|8956275|gb|BE230079.1|BE230079
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|8956207|gb|BE230011.1|BE230011
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|86413585|gb|CI019170.1|CI019170
EST:     ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: ATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|86834554|gb|CI344485.1|CI344485
EST:     GGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: GGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
EST: gi|313080737|gb|HO213534.1|HO213534
EST:     TTGAGATCCAG                         GCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC
genomic: TTGAGATCCAGgtaaatccac ... tttcttttagGCTAATGAGATGCTGCATCACAAGGCTAACCTGAATGGATACCTAGCATAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAGCGATACAGCTTACCTAACTCAAGAATAATGATCCATCAACCTCTCGGAGGAGCCCAAGGACAAGAGACTGATCTTGAGATCCAGgtaaatccacaaagttaaattgtgtttttatcaagatcaggacgacatctcaatagcaaataattaaccatatcattgtttctctcttgccggtatatgg

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC