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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaacatacatctctagcctctatctattgccactttgttagaccatgtaggaaatctaaaatcgaaattccatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT

Basic information

species Oryza sativa
transcript LOC_Os12g01449.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01449.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G396927_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------gttaacatacatctctagcctctatctat------tgccactttgtt-agaccatgtaggaaatctaaaatcgaaattccatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT---------------------
                                               ||||| ||| | ||    ||    |       |   | |||  | |||  ||| |   ||  | || || | | |  || |    |||||||  ||| ||||||||||||||||||||||| ||||| ||||||||||| ||||||||  |||| || ||||| ||| ||||||| |||||||||||||| |||||||                     
gtgtgcatctctagcatacactccaatttcgccaaacatgtgttaaaaacatgcatttttaattccttatgaaggtgggtatgattttactcagagtatgcacctaaa-tgaactcaataatttatttg--catgttgg--atatatcaaattggcatctgttcagCTTGCGAACAAGTATATGAAGAGGGTTGCATCAGAACTTGATGCGTTGGAAGGCACTGAGAAAGAGCCCAATAGAGAGTTTTTGCTTCTCCAGGGTGGCA

upper sequence: LOC_Os12g01449.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 7
-----------------------------------------------gttaacatacatctctagcctctatctattgccactttgttagaccatgtaggaa------atctaaaatcgaaattccatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT
                                               |  | ||| ||| | ||    ||    |  ||   | || |    | || || |       || | || || | |||  || |   | |||||| ||||||||||| |||||||||| ||||| || || ||||||||||| ||||||||| |||| || ||||| ||  ||||||| |||||||||||||| |||||||
gtttgcatctctagcaagcactccaattttgacaaacttgtgttaaagaaaccatgcatttttaattccttatgaaggcgggtgtgcttttacttggagtatgcacctatatgaactcaatattttatttg--tgtgttgg-aatagATCAAAGTGGCATCTGTCCAGCTTGCAAACAAGTATATGAAGAGGGTTGCCTCAGAACTTGATGCATTAGAAGGCACTGAGAAAGAGCCCAATAGAGAGT
















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|29625752|gb|CB630763.1|CB630763
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|89198800|gb|CI003537.1|CI003537
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|86415438|gb|CI069841.1|CI069841
EST:     GATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: GATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|86882487|gb|CI325851.1|CI325851
EST:     GGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: GGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|86480775|gb|CI123408.1|CI123408
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|86862736|gb|CI331634.1|CI331634
EST:     GGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGGCTGGCGAAGAAGTATATGAATAGGGTTGC
genomic: GGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCA-GCTGGCGAAGAAGTATATGAATAGGGTTGC
EST: gi|88850209|gb|CI091702.1|CI091702
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88830629|gb|CI078073.1|CI078073
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88841821|gb|CI081077.1|CI081077
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|29665532|gb|CB661807.1|CB661807
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88261521|gb|CI365097.1|CI365097
EST:     GTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATTAATAGGGTTGCC
genomic: GTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|89194967|gb|CI051080.1|CI051080
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88831297|gb|CI082107.1|CI082107
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGC---GAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88961895|gb|CI097048.1|CI097048
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88980888|gb|CI021016.1|CI021016
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|29675785|gb|CB672060.1|CB672060
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|88830857|gb|CI079291.1|CI079291
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|86481658|gb|CI124291.1|CI124291
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
EST: gi|29674414|gb|CB670689.1|CB670689
EST:     AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAG                         ATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC
genomic: AGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCC

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: 69 (upstream exon), 47 (downstream exon)
Score: 98

TGTTTATGCGCTACTTCGTACTAGAGACATGGCCATATCACGCTACAGGGAGTATGGAATACCGGTGGATTGGCTGTCTGATTCCGGGGTAGTTGGCAAGgttaacatac ... ttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaccatgtaggaaatctaaaatcgaaattccatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT
                atctaaa  putative branch site (score: 98)
              aaatctaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaacatacatctctagcctctatctattgccactttgttagaccatgtaggaaatctaaaatcgaaattccatcttgttatgttgggaatagATCAAATTGGCATCTGTTCAGCTGGCGAAGAAGTATATGAATAGGGTTGCCACAGAGCTAGATGCCTTGCAAGGCACCGAGAAAGAGCCCAACAGAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT