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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaatcaagcgtcatttttttttaagttggagaagttaaatcagtttgagttttcag

Basic information

species Oryza sativa
transcript LOC_Os12g01140.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G001457_T01 (Zea mays), 5'ss of exon 2
TGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaatcaagcgtcatttttttttaagttggagaagttaaatcagtttg-agttttcag-------------
||| ||||| |||||||||||||| || ||||| ||||| || ||| ||||||||||||||||  ||||||||||||||||||||||||| || |||  ||||| |||   || | |  | || |  || ||  | |  ||   |   ||||| | | |  |              
TGAGATGTTATATGGTTATACACCGTTCAGAGGGAAAACAAGACAAAGGACATTTGCTAATATTCTGCACAAGGATATCAGATTTCCTGCGAGCATACAGgtaa-taataaaaacatt-tattctagtaggtgagcgttgtggcaaatgtttgtaatgtatatatgttaattgtag
















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|29644412|gb|CB649419.1|CB649419
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|25806002|gb|CA761963.1|CA761963
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGACCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|66913937|gb|CX100785.1|CX100785
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29621738|gb|CB626749.1|CB626749
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|58695632|gb|CK084319.1|CK084319
EST:     CATTTGTTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29623925|gb|CB628936.1|CB628936
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29630467|gb|CB635476.1|CB635476
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCNGAGGCAGCTAATGTATAGGTTGCTACATAGGGACCC
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGC-GAGGCAGCTAATGTATAGGTTGCTACATAGGGATCC
EST: gi|29641401|gb|CB646408.1|CB646408
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29663823|gb|CB660098.1|CB660098
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|58689894|gb|CK078581.1|CK078581
EST:     CAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29678745|gb|CB675020.1|CB675020
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86896123|gb|CI330083.1|CI330083
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATA-GGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|18386007|gb|BM419206.1|BM419206
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGACCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|88299110|gb|CI570080.1|CI570080
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGGGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|88279055|gb|CI400055.1|CI400055
EST:     ATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGGTAATGTATAGGTTGCTACATAGGGATCCT
genomic: ATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86482520|gb|CI125153.1|CI125153
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86885168|gb|CI316928.1|CI316928
EST:     CATTTGCTAATATCTTGCACAA-GATATCAGATTTCCTG-TAGTATATCG                         TTCAGCCTAGC-GCGAGCCAGCTAATGTATAGGTTGCTACATA-GGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86417133|gb|CI031342.1|CI031342
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29630120|gb|CB635129.1|CB635129
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGACCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29634078|gb|CB639087.1|CB639087
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29672021|gb|CB668296.1|CB668296
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|88902162|gb|CI374770.1|CI374770
EST:     CAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|33680725|gb|CF308964.1|CF308964
EST:     AGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: AGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|58695041|gb|CK083728.1|CK083728
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29623926|gb|CB628937.1|CB628937
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86481030|gb|CI123663.1|CI123663
EST:     CTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGNCAGCTAATGTATAGGTTGCTACATAGGGGTCCT
genomic: CTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29624138|gb|CB629149.1|CB629149
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29646711|gb|CB651718.1|CB651718
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|88262034|gb|CI365610.1|CI365610
EST:     CATTTCCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATTTATAGGTTGCTACATA-GGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|33680724|gb|CF308963.1|CF308963
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAG
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAG
EST: gi|29622724|gb|CB627735.1|CB627735
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGACCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29674379|gb|CB670654.1|CB670654
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|86890159|gb|CI321336.1|CI321336
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATC-                         GTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT
EST: gi|29677072|gb|CB673347.1|CB673347
EST:     CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCG                         GTCAGCCTAGCGGCGAGGCAGCTAATATATAGGTTGCTACATAGGGATCCT
genomic: CATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCT

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: 75 (upstream exon), 66 (downstream exon)
Score: 31

TGAAATGTTGTATGGTTATACACCTTTTAGAGGAAAAACGAGGCAACGGACATTTGCTAATATCTTGCACAAGGATATCAGATTTCCTGCTAGTATATCGgtaagtaaat ... gagttttcagGTCAGCCTAGCGGCGAGGCAGCTAATGTATAGGTTGCTACATAGGGATCCTGCCAACAGGCTAGGGTCCTACGAGGGAGCCAATGAGATAAAAGGACATC




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