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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctctcttttaggtgtctatttaatatattttctcattttaatgtattatcatcctttacgtgttccag

Basic information

species Oryza sativa
transcript LOC_Os06g21390.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g21390.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G395842_T02 (Zea mays), 5'ss of exon 5
CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctctcttttaggtgtctatttaat---atattttc----tcattttaatgtattatcatcctttacgtgttccag
|||||||||||||| || |||||||||||||| |||||||| |||||||||||||| |||||||||||||| ||||| |||| ||| |||||| || ||||| | | || ||| | || |    |||||||    |||  |||   | | | | || | |   | ||||||
CATGCCTACAGAGATGGCCGCTTGGAAGAGGTAATACTGCGGCATCTTGATGCTGATGATGGAAGTACAGTAATTGCAAAAAGTATCAGgtatctgttctctatcaagtttctttgtattcttgtattttcaccctcaacttaccctctcaccttcatgtttctcttccag
















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|88215921|gb|CI215770.1|CI215770
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|29659494|gb|CB655769.1|CB655769
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|218493054|gb|FG951374.1|FG951374
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|58687235|gb|CK075922.1|CK075922
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86493358|gb|CI135991.1|CI135991
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86496021|gb|CI138654.1|CI138654
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86492823|gb|CI135456.1|CI135456
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86498369|gb|CI141002.1|CI141002
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|88227716|gb|CI227196.1|CI227196
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|33690378|gb|CF318617.1|CF318617
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAN                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86505484|gb|CI148117.1|CI148117
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|88842871|gb|CI371771.1|CI371771
EST:     TTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: TTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86501658|gb|CI144291.1|CI144291
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|89190314|gb|CI392364.1|CI392364
EST:     CGACATCTTGATGCTGACGATTGAAGTACAGTGATTGCCAAAAATAGTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86485014|gb|CI127647.1|CI127647
EST:     GGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: GGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|89181230|gb|CI045313.1|CI045313
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86500831|gb|CI143464.1|CI143464
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|86500426|gb|CI143059.1|CI143059
EST:     GGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: GGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
EST: gi|218488371|gb|FG949752.1|FG949752
EST:     CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAG                         GTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA
genomic: CGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctc ... cgtgttccagGTTGTCGGACTTCCTCAGTCGGTTACATCTTTAGGGACCAGTGACTGTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCCTACAGAGACGGACGCTTGGAAGAGGTCATACTGCGACATCTTGATGCTGACGATGGAAGTACAGTGATTGCCAAAAATATTAGgtatgtgctctcttttaggtgtctatttaatatattttctcattttaatgtattatcatcctttacgtgttccag

- - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG