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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgtaagcctgtaactcttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcag

Basic information

species Oryza sativa
transcript LOC_Os03g21080.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21080.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G110406_T01 (Zea mays), 5'ss of exon 9
CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgtaagcctgtaactcttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcag
 ||| ||||||| |||||||||||||| ||||| |||||||| ||||||||||| || || ||| |||| |||||||||||||||||||||||||| |||||        || ||| | | ||| ||||||||| |||   | | |   |  || |   |   | ||||| | | | || ||| ||| ||||| | ||   |    ||| | ||||||
ATTGAGAAATGAGCTAGAAGAACCACGGAGTTCTGAAGGTGATCAACTCCCAAGGCTTCAGAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgt-------gaggctgaatcccttctgcagaattggaaaggtctat-gggtttgtcactatcgtttgctcattt-tcttgtttttttagctaattcttttgatg--ctgcc-atgcag

upper sequence: LOC_Os03g21080.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G462803_T04 (Zea mays), 5'ss of exon 7
CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgtaagcctgtaactcttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcag
 ||| |||||||||||||||||||||| ||||| |||||||| ||||||||||| || |||||| |||| |||||||||||||||||||||||||| ||||| ||   | |  ||   ||| || ||||||||| | |  ||   ||| || || |   |   | ||||| | |  || |||  ||| || || | ||   | |   | || ||||||
ATTGAGAAATGAACTAGAAGAACCACGGAGTTCTGAAGGTGATCAACTCCCAAGGCTTCAAAGCTTGCAAAGGATACTCCAAGGAAGTGTGGCTGTGCAGgtgaggc-tgaatct---actttt-tgcagaattcggaagat---ttatgagtgtcactaccgtttgctcattttcttgcttcttttggccaattcttttgaca---tcaccatgcag

upper sequence: LOC_Os03g21080.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv11s0016g00100.t01 (Vitis vinifera), 5'ss of exon 29
CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgtaagcctgtaactcttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcag
 || || ||||| || ||||| || ||||| || ||||| || ||||||||| | ||||||||||| ||||| ||||||||||| ||||| || ||||| || || || | |        | ||||      |||      |  |||     ||     | | | ||    || |    |  | ||||||| | | | | || |              
ATTACGCAATGAGCTTGAAGAGCCTCGCAGCTCTGAAGGGGATCAACTCCCACGCCTCCAAAGCCTACAGAGAATACTCCAAGGCAGTGTTGCAGTTCAAgtgagttgcatggacccc-tttttgtttcccgttttgtttttcctttttccttgtaaccactgt-tgtcaatccaaac-caatattttgctta-tgtcataaga--------------

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|88844865|gb|CI022219.1|CI022219
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|3764134|gb|AU030634.1|AU030634
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|5003480|gb|AU068629.1|AU068629
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|58663644|gb|CK052330.1|CK052330
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTCAATAGTGGTGTATTAAGTGTGTGCACTGCA
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCA
EST: gi|58608909|gb|CK036942.1|CK036942
EST:     CAAGACTCCAAAGCCTGCAGAGGGTACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|3767208|gb|AU031318.1|AU031318
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|88328799|gb|CI646869.1|CI646869
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
EST: gi|27546784|gb|CA765043.2|CA765043
EST:     CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAG                         GTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC
genomic: CAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCC

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: 65 (upstream exon), 73 (downstream exon)
Score: 20

CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgta ... gacgatgcagGTAAATAGTGGTGTATTAAGTGTGTGCACTGCATTCTTATCTGGTGAGCCCGCAACTAGGCTCCGATCTCAAGAACTGCAGCAGCTCATCGCTGCATTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCGAAATGAACTAGAAGAACCACGCAGTTCGGAAGGTGACCAACTCCCAAGACTCCAAAGCCTGCAGAGGATACTCCAAGGAAGTGTGGCTGTTCAGgtaagctgtaagcctgtaactcttgtgcagaatttgaaccattttttaagaatgccttgagtatatgctcctctattttctttcttttgctaacttttacaaaaacctgacgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT