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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttctgtagtactttgactctgatgcgctttagacccgcagctggtatttgtggtgccctgttgtcaagtttttccttatcatgtatgtggccataacttattatactgattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG

Basic information

species Oryza sativa
transcript LOC_Os01g53520.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g53520.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G031308_T02 (Zea mays), 3'ss of exon 2
gtgagcttctgtagtactttgactctgatgcgctttagacccgcagctggtatttgtggtgccctg-ttgtcaagtttttccttatcatgtat-gtggccataacttattatactgat--tttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG
|||||||||||   |    |||   | |   |     || | |   |||  |   |   ||| ||| ||| || |         |   | |||     |   || ||||   |||| |  |||| |||||||| || |||||||||||||| ||||| || |||||  || | || ||  ||||||| || ||||||||||||||||| || || ||||| ||||| 
gtgagcttctgggat-tcctgatgttcaaatgaaaccgaactggttctgaaacagggcctgctctgattgccacgacacgagcaaaattttattacttcttcaatttatggcactgctgattttcagGTCCCCACCGAACATTCCTGAGGTCAAAATCCCTGAGGATGTGGCTGTTAATGTTGCCCTGTCACTGAGATATGAGATCAACAGGGGCTTTGCTACCTTA

upper sequence: LOC_Os01g53520.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G002786_T01 (Zea mays), 3'ss of exon 2
gtgagcttctgtagtactttgactctgatgcgctttagacccgcagctggtatttgtggtgccctgttgtcaagtttttcc--ttatcatgtatgtggccat-aacttattatactgat--tttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG
||||| ||  |   | | |    |   |       |  || ||       |    ||     |   ||| || |     |     |   | |||  |  | |  | || |  |  || |  |||| |||||||| ||||||||||||||||||||||| || |||||  || | || ||  |||| ||  | |||||||| |||||||| || || ||||| ||||||
gtgagatttcgggattcctgatgttcaaatgaaactgaactcgttctctatcgcagtctgctctaattgccatggcacacgagcaacattttataagatcttcgatttgtggtgttgctgattttcagGTCCCCACCAAACATTCCTGAGGTGAAAATCCCTGAGGATGTGTCTGTTAATGTTGCACTGACACTGAGATACGAGATCAACAGGGGCTTTGCTACCTTG
















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|218503591|gb|FG957184.1|FG957184
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|88342993|gb|CI641519.1|CI641519
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAG
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAG
EST: gi|58682983|gb|CK071670.1|CK071670
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACA
EST: gi|58673667|gb|CK062353.1|CK062353
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|29663265|gb|CB659540.1|CB659540
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|218484106|gb|FG945297.1|FG945297
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCA-AGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|7608733|gb|AU090514.1|AU090514
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|29663264|gb|CB659539.1|CB659539
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|29688123|gb|CB684398.1|CB684398
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|163922879|gb|EG712730.1|EG712730
EST:     CCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: CCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|2311112|gb|C27267.1|C27267
EST:     TCCCTGGCTGTCCTCTTCCCCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|218485421|gb|FG945032.1|FG945032
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|58695411|gb|CK084098.1|CK084098
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|10109165|gb|AU065308.2|AU065308
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|58686008|gb|CK074695.1|CK074695
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|58682578|gb|CK071265.1|CK071265
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|10794862|gb|AU108828.1|AU108828
EST:     CCACTTTCATCCACAA                         GTCCCCTCCCAAACATTCCTGAGGTGAAAATTCCCAGAGGACTTGACAGTA
genomic: CCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCT-CCAAACATTCCTGAGGTGAAAATT-CCAGAGGACTTGACAGTA
EST: gi|58596037|gb|CK006565.1|CK006565
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGA
EST: gi|218483599|gb|FG956155.1|FG956155
EST:     TCCCTGGCCGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|33678278|gb|CF306517.1|CF306517
EST:     TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: TCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
EST: gi|33693971|gb|CF322210.1|CF322210
EST:     GTCCAATGCCTCCACTTTCATCCACAA                         GTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA
genomic: GTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAA

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), 71 (downstream exon)
Score: 200

AGATCATGGAGTACCACCTCCTCACCTTGGTGTGCCACTGCCTCATTCTCTCCCTGGCTGTCCTCTTCCTCTGGTCCAATGCCTCCACTTTCATCCACAAgtgagcttct ... gattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaagtttttccttatcatgtatgtggccataacttattatactgattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG
                                         tactgat  putative branch site (score: 200)
                                               tttttt  CT-rich tract
                              ataacttattatactg  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcttctgtagtactttgactctgatgcgctttagacccgcagctggtatttgtggtgccctgttgtcaagtttttccttatcatgtatgtggccataacttattatactgattttttagGTCCCCTCCAAACATTCCTGAGGTGAAAATTCCAGAGGACTTGACAGTAAACATTGCCCTTTCTCTGAGATATGAGATCAATAGAGGTTTTGCAACCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA