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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G128877_T02 (Zea mays), 3'ss of exon 2
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaa--ccatagtcaatat-ctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
                            |  ||| |||   | ||     ||| | |   ||||   |||  |   ||   | ||| ||   | ||||| |   ||  | ||| |||| ||| | ||||||||||||||||| ||||||||||||||||| |||||||||||||||||  |||||
---------------------------gtatacaacat---ggcagatcatctaaaatacattactcgcccttgagaagttcctagacatggtgctaaccttgtaagcgctgtcattt-tgtgttacagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTTTTGAGAACGAGAAAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 2
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
|| || ||||   |   || |  | | |   | |  || ||  || | |     | |||   |   | || ||||||  ||  ||      ||||| ||   | ||  || ||||| || |  |||||||||||||||| ||||||||||||||||| |||||||| ||||||||| |||||
gtatgcaacatggc---agatcatctataataaattattcacccatgggcatgaaaagc---tcctttccagttgaatacacggta-----ctaacctcgcgagtgccgtcatttgcgtgttgcagTTTATGAGGAAACAGCTGGACTGATGGTTAATGACCCTGTATTGAGAACAAGAAAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 2
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
                                              |  || | ||| |   |  |    |  |  |     |   |||  || |    | |    ||| |  |     ||   |||||||||||||||||||||  |||||||||| || || || ||  | || |  |||
--------------------------------------------gtgcattttcataccgtgtgcaatattact--acttcaaactaattacttatgagaaactcattggttctctgcaattttagTTTATGAGGAAACTGCTGGCTTGATGGTTAATGATCCGGTGTTACGGACTCACAAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 2
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattata-tgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
                                              |  ||   ||| |   | || ||  | |  ||||   |  |     | ||  |||      | ||| | ||   ||   |||||||||||||||||||||  |||||||||| || || || ||  | || |  |||
--------------------------------------------gtgcatttccataccttctctaatgtttctgcaaactgcatccttctgcgaaactcat-----tcgttctctgca-attttagTTTATGAGGAAACTGCTGGTTTGATGGTTAATGATCCGGTCTTACGGACGCACAAG

upper sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 2
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
                  |||| ||| ||| |    |     |  |   || |  |   || |  | ||   || |       || ||||         |    |||| || |  ||||||  |||||||||| ||||| |||||  ||||||| ||||||||||||||  ||||||  |||
---------------catgtttttatatttgatctta-----atgcttcttgtattctaaagttcaagctcttttat------gttaatacaaggggataattttgtttttttgggtgtatttcagTTTATGAAGAAACAGCTGGTTTGATGGTGAACGACCCTGTTTTACGAACACACAAG

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|88431064|gb|CI574235.1|CI574235
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|58663310|gb|CK051996.1|CK051996
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|58673192|gb|CK061878.1|CK061878
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|88403893|gb|CI601303.1|CI601303
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|88717327|gb|CI740837.1|CI740837
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|58662103|gb|CK050783.1|CK050783
EST:     ATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: ATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|58663588|gb|CK052274.1|CK052274
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|58666816|gb|CK055502.1|CK055502
EST:     TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: TCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
EST: gi|27547953|gb|CA765929.2|CA765929
EST:     GGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAG                         TTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC
genomic: GGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACAC

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: 63 (upstream exon), 56 (downstream exon)
Score: 14

GGAATGGGAGGTGCTGCCATGTATGAACTCGTCCGTGTTGGGCACGATAATCTTATTGGAGAAATTATTCGTCTTGAGGGGGATTCAGCTACAATTCAAGgtgtggaaca ... tgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG
                  atctaac  putative branch site (score: 14)
                              aaatgttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggaacagctctttagtttctatctttaacagcatacagacacgagttctgatagcaattatatgcctgttgaaaccatagtcaatatctaacatcagaaatgttgttatttgtgtatcacagTTTATGAGGAAACTGCTGGACTGATGGTTAACGACCCTGTTTTGAGAACACGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA