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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttccttggttacttttcaccatcagaacaagctcttaaagcatattgagcaccaccgaccttcatatgatatgcttgtacagcaggcctgaatccccaaattttactgactggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTATGATAATGCAGAGGGTGACAGCCAGTTCCGAGAGGTGATAAAATCTCATG

Basic information

species Oryza sativa
transcript LOC_Os02g57640.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57640.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G008410_T01 (Zea mays), 3'ss of exon 7
gtatttccttggttacttttcaccatcagaacaagctcttaaagcatattgagcaccaccgaccttcatatgatatgcttgtacagcaggcctgaatccccaaattttactgac--tggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTATGATAATGCAGAGGGTGACAGCCAGTTCCGAGAGGTGATAAAATCTCATG
                                           | || ||       |||    | | |||        |  | |    |      |  | |||| ||||| ||  |||||||||||||||||||| ||||||||| | |||||||| | | | || ||||| ||||| |||||||||||| |||||||||| |||||||||| |   |     
-------------------------------------------gtattttcgttggtacctttttgcctatagc-----taaataatgtgtt---gttgctaaatcttactcacactggtgcagGAAAGTGACGATTACTGGAACACCCGAAGCTATCCGGACCGCGGAGTCCATGATCATGCAGAGGGTGTCAGCCAGTTCAGAGAGGTGATGAGCCCCTTCT
















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|29664586|gb|CB660861.1|CB660861
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|58676905|gb|CK065592.1|CK065592
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|29682210|gb|CB678485.1|CB678485
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|58689438|gb|CK078125.1|CK078125
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|88266396|gb|CI377298.1|CI377298
EST:     ATCAAAATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGA-                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: ATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|58675590|gb|CK064277.1|CK064277
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|86867600|gb|CI338135.1|CI338135
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|89171724|gb|CI720783.1|CI720783
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGNTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAAC
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAAC
EST: gi|88564590|gb|CI495307.1|CI495307
EST:     TCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCATAAGCTATTCAGGCAGCAGAGTCTAT
genomic: TCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|88507583|gb|CI435089.1|CI435089
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|88668291|gb|CI723030.1|CI723030
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTG
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTG
EST: gi|29686277|gb|CB682552.1|CB682552
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
EST: gi|89179860|gb|CI044139.1|CI044139
EST:     AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAG                         GAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT
genomic: AGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTAT

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: 62 (upstream exon), 74 (downstream exon)
Score: 75

GCTAGTGGTGCCAGGATCAAGATATCTGATAGGGGTGACTTCATTGCTGGCACATCTGAGAGgtatttcctt ... actggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTATGATAATGCAGAGGGTGACAGCCAGTTCCGAGAGGTGATAAAATCTCATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgatatgcttgtacagcaggcctgaatccccaaattttactgactggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTATGATAATGCAGAGGGTGACAGCCAGTTCCGAGAGGTGATAAAATCTCATG
                                        tactgac  putative branch site (score: 75)
                                  aaattttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttccttggttacttttcaccatcagaacaagctcttaaagcatattgagcaccaccgaccttcatatgatatgcttgtacagcaggcctgaatccccaaattttactgactggtgcagGAAAGTGACGATAACTGGAACATCAGAAGCTATTCAGGCAGCAGAGTCTATGATAATGCAGAGGGTGACAGCCAGTTCCGAGAGGTGATAAAATCTCATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG