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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaataccttcccttcgtatagttacccacaaataaaaaactacttatttagttttgacacatcagatatcattctgtaacttcttaccgcgtaacattt...

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgt----aataccttccctt----cgtatagttacccacaaataaaaaactacttatttagttttgacacatcagat--atcattctgtaacttcttaccgcgtaacattt
||||||||||||||||||||| || || |||||||| || |||||||| ||||||||| |||| | ||| || ||||| || ||||||||||| ||||||||    |  | |||| |||      | || || |       |   |  |  |  |   | |||| | ||  |||||  || |||   | |  ||   |   ||       
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaac--aattttcagac-ccagattaattattgaatgatgtcactcttagt-------

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA08G20830.3 (Glycine max), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaataccttcccttcgtatagttacccacaaataaaaaactacttatttagttttgacacatcagatatcatt-ctgtaacttcttaccgcgtaacattt---
 || ||||| || || |||||||| ||||| ||||| || || |||||||||   | |||||||||||| || |||||||| ||||| |||||  | |||||  ||        |  |      |||||    |     | ||    |||  | |    |  |  |||    || || ||| |  |||  |  |   | |    
GTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTTAGTCGTGATTACATGACCTTAAAGgttttagagctttattattccaaaacccatgcttctgtcaataaagcttt--tctgagtattttggatggagttactctaaat--ttattgaattgaactccat

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgt---aataccttcccttcgtatagt-tacccacaaataaaaaactacttatttagttttgacacatcagatatcattctgtaacttcttaccgcgt--aacattt---
 |||||||| || || ||||||||||| || ||||| || ||||| ||||| |||| |||||| |||||||| |||||||||||||| ||||| ||||||||   ||  | |||  |||   | || ||        | |       |  ||  || | | |  | | || |  | |||||  |  | |||||   |   || |||   
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTTAGTCGCGATTACATGACGCTCAAGgttggaaatcattcggttccctttgtgtatatttttctgattgtgggccaatagaggtct-attctttagtt--ctttctgatatcttttaccctttttgacgtttcag

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacct-tcccttcgtatagttacccacaaataaaaaactacttatttagttttgacacatcagatatcattctgta-acttcttaccgcgtaacattt
 |||||||| || || ||||||||||| || ||||| || || || |||||||| | |||||||||||  || || ||||| ||||| ||||| || |||||      | |||| |  |    ||     ||  |  | |  |   | |  |  |||  ||  ||    |    | | ||    |  |   |  ||   |  
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTCAGTCGAGATTACATGACCCTTAAGgtttgggttatcccatttttctattcatttcagcttcacatttgact-tgaaacttttgcaattctatcactgctatatatgggtgctttagtctagagtg-

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgta-ataccttcccttcgtatagttacccacaaataaaaaactacttatttagttttgacacatcagatatc-attctgtaacttcttaccgcgtaacattt-
 |||||||| || |||||||||||||| || ||||| || |||||||| ||||||| |||||||||| |  | |||||||| ||||||||||| || |||||  ||   |||   |  |  ||| |        |  ||   | |  ||  |  ||||  |   || ||||  |  || ||  |  |    || ||   |   
TTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTTAGTCGTGATTATATGACACTTAAGgttcattaattcttattttccagtgatttt--gtttgaagtgttcacatcaaagtttgcaattgcatatatggaaactatagata-tgcttgcatactctgcg

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaataccttcccttcgtatagttacccacaaataaaaaactacttatttag------ttttgacacatcagatatcattctg-taacttcttaccgcgtaacattt
 |||| ||| || || ||||||||||| || ||||| || || || || |||  || ||| ||||||||||| |||||||||||||| |||| ||| |||||  |  || |  ||  | |  |    |   ||||    | |  | |  |          ||    |||   | ||  || || |||||     | ||   |     
TTCAAAATCTTTTTTCACAGAGATAATTGCTTCAATTTCAGACATTAAGTTTGGAAAGGACGGAAGATACATACTTAGTCGCGATTACATGAATCTGAAGgt--ttactcctatttatctgctatttctttaatatgttatttttgacatgaggtattcattattgcattgtagatagttgtggtaactgtaggctgctgca-----

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|58655643|gb|CK044323.1|CK044323
EST:     ATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGG-TCGT
genomic: ATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58675521|gb|CK064208.1|CK064208
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|66913089|gb|CX099937.1|CX099937
EST:     ATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGAACTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: ATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|218501369|gb|FG965487.1|FG965487
EST:     TTCAANGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTCAA-GGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATAGGGCTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGA
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGA
EST: gi|25807737|gb|CA763698.1|CA763698
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|88411135|gb|CI606354.1|CI606354
EST:     ATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: ATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAG                         CTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT
genomic: TTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaatacctt ... ttttcctcagCTATGGGATCTAAACATGGATTCAGGTCCTGTTTCAACCTTCCAGGTTCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgtaataccttcccttcgtatagttacccacaaataaaaaactacttatttagttttgacacatcagatatcattctgtaacttcttaccgcgtaacattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA