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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTACAAGAGCCTTGGACTTTAATTATCGATGATGGATTGGCAGCTTCATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttaccttaatcaatcaattggatcatatactatattgtctttaaaaatgggagggaattccttgaatctaaatatttaaccaaactttgaggttc...

Basic information

species Oryza sativa
transcript LOC_Os08g36774.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 16
AGTTTACAAGAGCCTTGGACTTTAATTATCGATGATGGATTGGCAGCTTCATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttaccttaatcaatcaattggatcatatactatattgtctttaaaaatgggag--ggaattccttgaatc--taaatatttaaccaaactttgag-gttc--------------
|||||||||||  | |||||| |||| || |||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||||| ||| ||||||||||||||| | | ||||| |||||     | |   |       |  | | |  ||  |  | || |    | ||   |  |||| ||  || |||    | ||||              
AGTTTACAAGAAGCCTGGACTCTAATAATTGATGATGGATTGGCGGCTTCATTTGTGGCCCCGGCTACTGATTCGTTAGAAGATGACAGCCAACTAACCAgtaagttaacctcatcaa-caattcagatacacgatggtgctcccctgataccggatgctgcaagttaaaggatgcgtgcatatatactcatactgaatgtgttctttgtggagtgcag
















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|88253666|gb|CI352292.1|CI352292
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|86497823|gb|CI140456.1|CI140456
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGATCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|29642058|gb|CB647065.1|CB647065
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|86494816|gb|CI137449.1|CI137449
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88971586|gb|CI388831.1|CI388831
EST:     ATTTGTTGCTCCAG-TACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATTTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|29633614|gb|CB638623.1|CB638623
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|89174515|gb|CI110713.1|CI110713
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGACGCAGAATGAGGAGCTTGGCTTGAAT
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGA-GCAGAATGAGGAGCTTGGCTTGAAT
EST: gi|86867747|gb|CI342698.1|CI342698
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88835926|gb|CI371031.1|CI371031
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGGCTGGGAGCAGAATGAGGAGCTTGGCTTGAAT
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAG-CTGGGAGCAGAATGAGGAGCTTGGCTTGAAT
EST: gi|86869122|gb|CI335689.1|CI335689
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88476939|gb|CI414210.1|CI414210
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88225974|gb|CI225890.1|CI225890
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88219195|gb|CI220468.1|CI220468
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88903530|gb|CI089068.1|CI089068
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88501970|gb|CI429476.1|CI429476
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|88471384|gb|CI408655.1|CI408655
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|89187077|gb|CI047144.1|CI047144
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|86426635|gb|CI071732.1|CI071732
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|38474287|gb|CF958419.1|CF958419
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|29633610|gb|CB638619.1|CB638619
EST:     ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
EST: gi|86825556|gb|CI361736.1|CI361736
EST:     ATTTTTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCA                         TTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG
genomic: ATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATG

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: 45 (upstream exon), 73 (downstream exon)
Score: 5

AGTTTACAAGAGCCTTGGACTTTAATTATCGATGATGGATTGGCAGCTTCATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttacc ... aaatttccagTTGAGGAGTATGTGAGGAGCTGGGAGCAGAATGAGGAGCTTGGCTTGAATGACATGGACACATCGTCTGCTGACGCCGCCTACAACACCACCAACCCATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTACAAGAGCCTTGGACTTTAATTATCGATGATGGATTGGCAGCTTCATTTGTTGCTCCAGCTACCGATTCTTTAGAAGATGACAACCAGCTAACCAgtaagttaccttaatcaatcaattggatcatatactatattgtctttaaaaatgggagggaattccttgaatctaaatatttaaccaaactttgaggttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgggagg