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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagaggggcttctcctcacccggattgatcgaacccttgcagatccgcggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT

Basic information

species Oryza sativa
transcript LOC_Os03g10190.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G124439_T01 (Zea mays), 3'ss of exon 1
gtaagagagggg-cttctcctcacccggattgatcgaacccttgcagatccgc-ggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
||||| |      || ||| | |||| |      |    |||| |  |   || |||| ||||  |  ||   | ||  |  || ||||||||||||||||| || || |||||||||||||| |||   ||||||||| | |||||||||||||| || 
gtaagtgtccactctcctcgttaccctgccc--ccatctccttcctcacaggctggtctctgactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTTAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCC

upper sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G014367_T01 (Zea mays), 3'ss of exon 1
gtaagagagggg-cttctcctcacccggattgatcgaacccttgcagatccgc-ggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
||||| |      || ||| | |||| |      ||   |||| |  |   || |||| ||||  |  ||   | ||  |  || ||||||||||||||||| || || ||||||||||||||||||   ||||||||| | |||| ||||||||| |||
gtaagtgtccactctcctcgttaccctgccc--ccgtctccttcctcacaggctggtctctgactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTGGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGACAAGCTCAAAGCT

upper sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G172101_T01 (Zea mays), 3'ss of exon 1
-------------gtaagagaggggcttctcctcacccggattgatcgaac-ccttgcagatccg---cggtccctgatccctagctat--acttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
                         ||   || | |||   |   || |||  ||| |||||||    ||||| ||||  |  ||   |   | ||   || ||||||||||||||||| ||||| ||||||||||||||||||   ||||||||| | || ||||||||||| || 
gtaagtgtccactcccctcattaccctggcccccgcccccctccctcaaacgtcttccagatcccggtcggtctctgactctcagtggttcgcgtcgctgctgcagGGCAGTTCGAGCTGGACAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATTGGCAAGCTCAAAGCC

upper sequence: LOC_Os03g10190.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G355297_T01 (Zea mays), 3'ss of exon 1
gtaagagagggg-cttctcctcacccggattgatcgaacccttgcagatccgc-ggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT---------
||||| |      || ||| | |||| |       |   |||| |  |   || |||| || |  |  ||   | ||  |  || ||||||||||||||||| || || ||||||||||||||||||   ||||||||| | |||||||||||||| ||          
gtaagtgtccactctcctcgttaccctgccc--ctgtctccttcctcacaggctggtctctaactctgaggcgtcctcat--gctgcagGGCAGTTCGAGCTAGATAAGATCCGGCAGGAGCTCAACGCTACCAGCAAGAAGATCGGCAAGCTCAAAGCCATACGTACC

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|88718099|gb|CI741609.1|CI741609
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|29678008|gb|CB674283.1|CB674283
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCC--A                         -G-A-TTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88318126|gb|CI629407.1|CI629407
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88422886|gb|CI615186.1|CI615186
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88317322|gb|CI627971.1|CI627971
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88359270|gb|CI679792.1|CI679792
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88393472|gb|CI619764.1|CI619764
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|58694443|gb|CK083130.1|CK083130
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88343285|gb|CI627245.1|CI627245
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCCCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|58590088|gb|CF988396.1|CF988396
EST:     GTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGCAC-AGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: GTCGAGCTCGTCGACGAGGTCATCGCCCTCGACG-ACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88306229|gb|CI636613.1|CI636613
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|2443078|gb|C74849.1|C74849
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88357315|gb|CI622164.1|CI622164
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGAAAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88417551|gb|CI581574.1|CI581574
EST:     CGTCGAGCTCGGCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
EST: gi|88358010|gb|CI650746.1|CI650746
EST:     CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGA                         GGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG
genomic: CGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGG

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: 74 (upstream exon), 70 (downstream exon)
Score: 9

GGCGGCGACCCGGAGCTGATCCGCAAGTCGCAGCGCAACCGCTCCGCCTCCGTCGAGCTCGTCGACGAGGTCATCGCCCTCGACGACCAGTGGCGCCAGAgtaagagagg ... ttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgaacccttgcagatccgcggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT
                       ccctgat  putative branch site (score: 9)
                                         cttcttcgcc  putative PPT
                                     tatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagaggggcttctcctcacccggattgatcgaacccttgcagatccgcggtccctgatccctagctatacttcttcgccgcagGGCAGTTCGAGCTCGACAAAATCCGGCAGGAGCTCAACAAAACCAGCAAGGAAATCGGCAAGCTCAAGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA