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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCTGCACACACATCTAATTCAAGATATGCTTTCTATCTGTCGTGAAACATTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgctttcccttttctgttcatagtttccatgtacctcattgttatcgtatacatatatgtcttagccctcaataatttatgcactttctgctaa...

Basic information

species Oryza sativa
transcript LOC_Os06g33710.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G047867_T01 (Zea mays), 5'ss of exon 9
GGCTGCACACACATCTAATTCAAGATATGCTTTCTATCTGTCGTGAAACATTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgctttcccttttctgttcatagtttccatgtacctcattgttatcgta-tacatatatgtcttagccctcaat-aatttatgcactttctgctaa
||||||||||||||||||| || ||||||||| ||||||||||  | |||||||| || |||||||| |||||||||||||| ||||| || ||||| ||||    |||  |    ||| |    ||  | | ||||| | |  || |     || ||  | | ||  ||  |||           ||       |    | 
GGCTGCACACACATCTAATCCAGGATATGCTTGCTATCTGTCGACAGACATTCAAAGGTGCTGTGCACTATGCCTGGACAAGTGTTCCAACATATCCCAGgtattatgcactaatattttt-ccaattctctgcatgtgcatttttttctctttagtaattttctgagttgtccccaggccggcccatatgggagcctaca-

upper sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA06G13210.2 (Glycine max), 5'ss of exon 9
GGCTGCACACACATCTAATTCAAGATATGCTTTCTATCTGTCGTGAAACATTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgctttcccttttctgttcatagtttccatgtacctcattgttatcgtatacata-tatgtcttagccctcaataatttatgcactttctgctaa---------------
|||| || |||||||| |||||||||||| | ||||| ||||| ||||||||||| ||  |||| | |||||| ||| |||| || || || ||||| ||||  |||||  |        || | |||  ||  || ||  ||  |  ||   |  |  |  | ||   |  |  |||  |||| ||   |||  | |                  
GGCTTCATACACATCTTATTCAAGATATGATCTCTATTTGTCGAGAAACATTCAAAGGTTCTGTACGTTATGCATGGGCAAGTGTACCAACGTATCCAAGgta-gttgcacttttcaacgtgctgataaatttaatatatttctgttctactttgaagttcctttgatgtcactttcagaaattcattatcttctttcctcttccttggcatgcag

upper sequence: LOC_Os06g33710.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 9
GGCTGCACACACATCTAATTCAAGATATGCTTTCTATCTGTCGTGAAACATTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgctttcccttttctgttcatagtt--tccatgtacctcattgttatcgtatacatatatgtcttagccctcaataatttatgcactttctgctaa
|||| ||||||||||| ||||| |||||||||||||| ||||||||||||||||||||  | || |||||||| ||| |||| |||||||| ||||| ||||   |    |     | ||| |  || | |  |   | |||    || || || |     ||| || | |  ||   ||| ||    |   |||     | 
GGCTCCACACACATCTTATTCAGGATATGCTTTCTATTTGTCGTGAAACATTCAAGGGTTCGGTCCATTATGCATGGGCAAGTGTTCCTACATATCCAAGgta-atcatgtattgatctctatatatggctaattgctctactgattttttctctttggtctat-tgccctttccagaaatgataagggtgatttggaagat

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|29660328|gb|CB656603.1|CB656603
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29681268|gb|CB677543.1|CB677543
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|33686636|gb|CF314875.1|CF314875
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGG-TTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACT
EST: gi|29681921|gb|CB678196.1|CB678196
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|2311358|gb|C27513.1|C27513
EST:     ACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: ACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|86494920|gb|CI137553.1|CI137553
EST:     AGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGGTGAACT
genomic: AGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCA-GTGAACT
EST: gi|86419330|gb|CI054131.1|CI054131
EST:     AGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: AGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29639075|gb|CB644084.1|CB644084
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|8527728|gb|AU092543.1|AU092543
EST:     GACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: GACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29665561|gb|CB661836.1|CB661836
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29689098|gb|CB685373.1|CB685373
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29677613|gb|CB673888.1|CB673888
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|86492595|gb|CI135228.1|CI135228
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29661774|gb|CB658049.1|CB658049
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29657895|gb|CB654170.1|CB654170
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|29674258|gb|CB670533.1|CB670533
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|38468529|gb|CF952660.1|CF952660
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|88828363|gb|CI000472.1|CI000472
EST:     CTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: CTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
EST: gi|9865343|gb|AU101093.1|AU101093
EST:     TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAG                         TGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT
genomic: TTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgct ... gcatttgcagTGGTGTCATTGGTTTTTTGCTATGTGCGAAAGAAGGTCCAGCAGTGAACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCTGCACACACATCTAATTCAAGATATGCTTTCTATCTGTCGTGAAACATTCAAGGGAGCTGTGCATTATGCCTGGACAAGCGTTCCTACCTATCCTAGgtccgttgctttcccttttctgttcatagtttccatgtacctcattgttatcgtatacatatatgtcttagccctcaataatttatgcactttctgctaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT