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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGCTGAGAGAGCGGGGCTTGCACCATGACTACGTCACTGCGTTACTGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactcttttgccaactggcgcacacgtttctcccatcttgctccaaatttataaaatcactatatcatcatgttcgtatttcctatgcattgcaagttt...

Basic information

species Oryza sativa
transcript LOC_Os10g26140.3
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g26145.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G444692_T02 (Zea mays), 5'ss of exon 11
GGACATGCTGAGAGAGCGGGGCTTGCACCATGACTACGTCACTGCGTTACTGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactcttttgccaactggcgcacacgtttctcccatcttgctccaaatttataaaatcactatatcatcatgttcgtatttcctatgcattgcaagttt
|||||||||||| ||||| ||| |||| || |||||||| |||||| | |||||||| || ||| || ||||||| || ||||| || |||||||||||||| ||    |      ||   | | | || | ||  ||    | || |     |  |               |  |                        
GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggctttgctttgattcgctc-ttccccctttcaccttgcatacgccgatgactgacgcgaggattcgcccag----------------------
















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|88255830|gb|CI353701.1|CI353701
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|88849149|gb|CI087671.1|CI087671
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86502356|gb|CI144989.1|CI144989
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|89186084|gb|CI047953.1|CI047953
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86477411|gb|CI120044.1|CI120044
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|94362431|gb|CI052426.1|CI052426
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|89192800|gb|CI050098.1|CI050098
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86862123|gb|CI330695.1|CI330695
EST:     GAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: GAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|58687502|gb|CK076189.1|CK076189
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86482162|gb|CI124795.1|CI124795
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|87013138|gb|CI281652.1|CI281652
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86884727|gb|CI313106.1|CI313106
EST:     GCAAGGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: GCAA-GACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86827328|gb|CI270972.1|CI270972
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|29621826|gb|CB626837.1|CB626837
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|87016317|gb|CI271728.1|CI271728
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86832490|gb|CI344740.1|CI344740
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86895290|gb|CI331224.1|CI331224
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|16578849|gb|BI812944.1|BI812944
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|88844852|gb|CI022206.1|CI022206
EST:     GCAAGACGGATACCACCTGGAGGCTCTTCCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: GCAAGACGGATACCACCTGGAGGCTCTT-CGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|29634117|gb|CB639126.1|CB639126
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86478805|gb|CI121438.1|CI121438
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86482103|gb|CI124736.1|CI124736
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86868248|gb|CI331938.1|CI331938
EST:     ACGCTAG-AAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGGCTGTGGCCATAAA
genomic: ACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAA-GCTGTGGCCATAAA
EST: gi|86431426|gb|CI085037.1|CI085037
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|88460014|gb|CI526870.1|CI526870
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86840823|gb|CI335026.1|CI335026
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|88265009|gb|CI368783.1|CI368783
EST:     CGCTACGCTAGAAAATACAAG                         TTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: CGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86437670|gb|CI119590.1|CI119590
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|286811|gb|D15618.1|D15618
EST:     TTCAAGACGGATACCACCTGGAGGCTCTTNG-TACGNTAGAAAATACAAG                         GTAATAACTGTGCAGC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGC
EST: gi|87016228|gb|CI271639.1|CI271639
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|29630282|gb|CB635291.1|CB635291
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|29669543|gb|CB665818.1|CB665818
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86481413|gb|CI124046.1|CI124046
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|88475975|gb|CI413246.1|CI413246
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86895616|gb|CI315935.1|CI315935
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCTCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|89195851|gb|CI007270.1|CI007270
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
EST: gi|86437949|gb|CI119869.1|CI119869
EST:     TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAG                         GTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC
genomic: TGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactctttt ... actgttccagGTAATAACTGTGCAGCCTGTCCTGTTCTTGGAGAAAGCTGTGGCCATAAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATGCTGAGAGAGCGGGGCTTGCACCATGACTACGTCACTGCGTTACTGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactcttttgccaactggcgcacacgtttctcccatcttgctccaaatttataaaatcactatatcatcatgttcgtatttcctatgcattgcaagttt

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG