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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatgttgttcactagtgtttgcgagaggaattctcaatctctaaaactgtgtagcatggcagtatccatgtacttcgttatgtgcttatcttag...

Basic information

species Oryza sativa
transcript LOC_Os06g45660.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45660.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G143767_T01 (Zea mays), 5'ss of exon 4
GGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatgttgttcac--ta-gtgtttgcgagaggaatt--ctcaatctctaaaactgtgtagcatggcagtatccatgtacttcgttatgtgcttatcttag
 ||||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||    ||||||||| | || ||| ||||||||| ||| | | | ||||||  || |||   | |     | |      |  ||  |||||  | || |||| |    ||  || || | | |   || |   |||||
AGATGAAAATGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCACGTTCTAGTCATCCCAAAAGCGAGAGATGGGCTAACCGGATTAGACAAGgcatgta-tctcgttcacattacgtgccggtgcacaaactgagtcgagcctggaaaacattttaccatgact---tctgtg-acattgctgcatgtt---cttag
















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|38480548|gb|CF964637.1|CF964637
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|218505045|gb|FG968801.1|FG968801
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88572461|gb|CI664032.1|CI664032
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCG
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCG
EST: gi|38477525|gb|CF961658.1|CF961658
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33815382|gb|CF333545.1|CF333545
EST:     GTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: GTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|58596640|gb|CK007168.1|CK007168
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33689071|gb|CF317310.1|CF317310
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33822248|gb|CF336938.1|CF336938
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|38475488|gb|CF959621.1|CF959621
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|38475613|gb|CF959746.1|CF959746
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88334078|gb|CI641129.1|CI641129
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCG
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCG
EST: gi|33689070|gb|CF317309.1|CF317309
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88283761|gb|CI405207.1|CI405207
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|25797786|gb|CA753747.1|CA753747
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGGATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|55414604|gb|CV726980.1|CV726980
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|55414535|gb|CV726911.1|CV726911
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|38481086|gb|CF965175.1|CF965175
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|163925430|gb|EG713343.1|EG713343
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88382349|gb|CI633207.1|CI633207
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGC
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGC
EST: gi|5004087|gb|AU069236.1|AU069236
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33657720|gb|CF280334.1|CF280334
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88345287|gb|CI655747.1|CI655747
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATA
EST: gi|33689232|gb|CF317471.1|CF317471
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88376801|gb|CI639126.1|CI639126
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAAT
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAAT
EST: gi|2317371|gb|C22425.1|C22425
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33823879|gb|CF337751.1|CF337751
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33656833|gb|CF279447.1|CF279447
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88380875|gb|CI634900.1|CI634900
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCAT
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCAT
EST: gi|88238598|gb|CI238447.1|CI238447
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|88992474|gb|CI035594.1|CI035594
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|11442620|gb|BF430523.1|BF430523
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|55435458|gb|CV730859.1|CV730859
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33815380|gb|CF333544.1|CF333544
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|33659581|gb|CF282194.1|CF282194
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|112785873|gb|EE591589.1|EE591589
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
EST: gi|87004366|gb|CI298898.1|CI298898
EST:     ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAG                         GCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA
genomic: ATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 67 (downstream exon)
Score: 68

GGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatg ... atatttttagGCTGAACCAAGGCATGTCGAAATTCTGGGCTATCTTCTATACGCCGCGAAAATAGTGGCTGAGAAGGAAGGTATAGCTGAAGGGTACCGTGTCGTCATAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGAGAAAGTGCTGGCATTTAGAGATATTAATCCACAAGCCCCTGTGCATGTTCTAGTCATCCCAAAGATAAGAGATGGGTTGACTGGACTAGACAAGgtatggaatgttgttcactagtgtttgcgagaggaattctcaatctctaaaactgtgtagcatggcagtatccatgtacttcgttatgtgcttatcttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG