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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttgcatagttctgtttccaatttgtatgtccactagttactgcttttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT

Basic information

species Oryza sativa
transcript LOC_Os03g22880.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 6
gttagttgcat--agttctgtttccaatttgtat-gtccactagttactgcttttgctgaaagaacttgct------------gccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
|||||||  |   || |||||  ||    ||| | ||   |||  |  | ||  | |  |||| |  |  |             |  || | | || ||||||| |    ||| | ||||||||||||||| | ||||||||||| |||||| |  | || |||||||||||||||||||| ||||||||||||||||||||
gttagttcgaggaagctctgtcaccggactgttttgtatgctaagt-ttactcattccaaaagcatctttttgattgttttgtactgtactcttgacttcagAGGCTAGCACCTCTGTCTTTGGGCAAAAGTTGCGTGAGCAAGTCGAGGAGAGACTGGAATTCTATGACAAGGGTGTTGCGCCTCGTAAAAACCTTGATGT

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 6
gttagttgcat--agttctgtttccaatttgtat-gtccactagttactgcttttgctgaaagaac-------------ttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
|||||||  |   || |||||| ||    ||| | ||   ||| |   | ||    |  |||| |              ||    |  ||| || |  ||||||| |   |||| | ||||||||||||||| | || |||||||| |||||| |  | || |||||||||||||||||||| ||||||||||| ||||||||
gttagttctaggaagctctgttaccggactgttttgtatgctattgtttcctcgatccaaaagcatcatcttgattgttttatacctttatatttggtttcagAGGCTAGTACCTCTGTCTTTGGGCAAAAGTTGCGCGAGCAAGTCGAGGAGAGACTGGAATTCTATGACAAGGGTGTTGCGCCTCGTAAAAATCTTGATGT

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 6
----gttagttgcatagttctgtttccaatttgtatgtccactagttactgcttttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
    |||  ||||||| |    ||  ||  ||  ||| |      |  |   || |  |||       |  ||   ||| ||  ||| ||||    | |||  | || |||||||| || || ||||||||||||||||| ||  | ||||| ||||||||||| ||||| ||||| || ||| | |||||
gtttgtttcttgcatattcactttagcatatttcatggctgtacatagccctttgtcatga-------ttttgtggtatctt--aatgcagAAAAGGGTACTACTGTTTTTGGGCAGAAACTCCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 6
gttagttgcata-gttctgtttccaatttgtatgtccactagttactgctt--ttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
||| ||| | ||  ||    ||  |       | | |  || ||| | | |  |||||        |   |    | |  ||  || ||||    | |||  |    |||||| | || || ||||||||||||||||||||  | || || ||||||||||| ||||| |||||||| ||| | |||||
gtttgtttcttacatttaaattttagcaatcttatgccttacttagtacctcattgcttgttaggatgattttgttgtactgtgatgcagAAAGGGGTACTACTACTTTTGGGGAGAAACTCCGTGAGCAAGTTGAGGAGCGACTTGATTTTTATGACAAGGGAGTTGCCCCTCGTAAGAACATAGATGT

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 6
----gttagttgcatagttctgtttccaatttgt-atgtccactagttactgcttttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
    |||  || |||| |    ||  |||| | | ||| |   ||  ||   ||||    |  |  | ||       ||  |   ||| ||||    | |||  | || |||||| | || || ||||||||||||||||| ||  | ||||| ||||||||||| ||||| ||||| || ||| | |||||
gtttgtttctttcatattcactttagcaatatctcatggctg-tacatagcacttt----gtcatgatttagctttgtacctc--aatgcagAAAGGGGTACTACTGTTTTTGGGGAGAAACTGCGTGAGCAAGTTGAGGAACGACTTGACTTTTATGACAAGGGAGTTGCCCCTCGCAAGAACATAGATGT

upper sequence: LOC_Os03g22880.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 6
gttagttgc-atagttctgtttccaat--ttgtatgtccactagttactg--cttttgctgaaagaacttgctgc-catattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
|| |||| | |||  |   | |    |  ||  || ||   | | |       ||||     |  || ||| ||| ||   ||  |  | |||||      ||| | || |||||| | || || ||||| ||||||||||||||  | || || |||||||||||  |||||||||| |||||| |||||||
gtaagtttctataaattcttatatggtcatttcatttctcatggatggcaactttttatctgataaatttgttgcacaatcttctgtgtgcagAGAGTAACACCACGGTTTTTGGGGAGAAACTCCGTGAACAAGTTGAGGAGCGACTCGAATTTTATGACAAGGGAATTGCACCTCGGAAAAACATTGATGT

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|27546695|gb|CA767278.2|CA767278
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|86496816|gb|CI139449.1|CI139449
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|218493558|gb|FG968381.1|FG968381
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|218498396|gb|FG949417.1|FG949417
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|27576278|gb|CA998972.1|CA998972
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCA
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCA
EST: gi|396941561|gb|HO188770.1|HO188770
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|27554440|gb|CA998340.1|CA998340
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|88294525|gb|CI525261.1|CI525261
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|58657958|gb|CK046638.1|CK046638
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|88417722|gb|CI535881.1|CI535881
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|89168282|gb|CI109486.1|CI109486
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
EST: gi|58676954|gb|CK065641.1|CK065641
EST:     ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAG                         AGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC
genomic: ATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGC

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), 67 (downstream exon)
Score: 21

TCATCCTTCATTGGCCGTGCTTCAACCAAGAACAAAGGCAGAATGGCTAGATATCTGGCGAACAAGTGCTCCATTGCATCACGCATTGATTGTTATTCAGgttagttgca ... tggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccactagttactgcttttgctgaaagaacttgctgccatattttggaattcagAGTCAGCTACCGCAGTCTTTGGGCAAAAGCTTCGTGAGCAAGTTGAGGAGCGGTTAGACTTCTATGACAAGGGTGTTGCACCTCGTAAAAACCTTGATGT
                                       atatttt  TA-rich tract