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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA

Basic information

species Oryza sativa
transcript LOC_Os11g08210.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G123667_T04 (Zea mays), 3'ss of exon 1
-----------------gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttgg--aattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
                  | | |   ||| |  |    |  |  |||       |  |      |     |  |    || |  |||     ||     | |||||||||| |||| | || |||||||||||||||||||||||||||||||| ||||| ||||||||||| ||     |||                         
gtacgtcgaacaatcggatcatcgtcagcgagtgttagtt-atccgagctagctaggtgacgaccccgcgctgacctcatcagCTGGCATGGTGATCGGTGGTTGCAGAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGC-------------------------

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G123667_T05 (Zea mays), 3'ss of exon 1
-----------------gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttgg--aattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
                  | | |   ||| |  |    |  |  |||       |  |      |     |  |    || |  |||     ||     | |||||||||| |||| | || |||||||||||||||||||||||||||||||| ||||| ||||||||||| ||     |||| ||| ||||||| ||||| |||||
gtacgtcgaacaatcggatcatcgtcagcgagtgttagtt-atccgagctagctaggtgacgaccccgcgctgacctcatcagctggcatggtgatcggtggttgcagAGAAGGCGTTCGGTGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGCGACCGCAAGTACCCGAATGGCTCCAGGCCTAACCGGGCGGCCGGGACAGGGTA

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G26480.1 (Glycine max), 3'ss of exon 1
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaatt-----caattaattggggat---ttggaattgt----tgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
 |||      ||| ||     ||  ||      ||   || |||     | ||    ||      || |||||    ||    |||  ||||    || ||  | |||  ||   || ||||| |||||||| || ||| ||||| ||||||| ||||||||||||||   |||||||||| || | |||||||| || ||
-taaaatcttgcacaaattattctcataattctgaaataaatgataataacttttttttattgataaataatttaatatattctggtgttgtgttatgtagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGGACCGGATA

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G42800.1 (Glycine max), 3'ss of exon 1
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
          | || |  |  |  ||        |     ||    |  | |   |||||| | | ||   || |||  |||||  |||    |||       || ||||| |||||||||||||| || || ||||||||||| |||||||||||     |||||||| |||||||||| || || ||
----------gtaacattatcttcaacttctgatatattcttattcttaattcttaattcattcattttttgaattgttattgt-acagGATTGGCTTCCTACGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCGAACGGTTCCAGGCCGAACCGGGCGGCGGGAACCGGTTA

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 1
--gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaat--tcaaattcaattaattggggatttgg-aattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
        |    |  | |    |||  | |  |  |   ||||  | | | ||  |  | ||||||| ||||   ||  |    |   |||||| |  |   |    || ||||| || ||||||||||| || || ||||||||||| |||||||||||    ||||||||| | || || || |  || ||
gttcgtttagtttcttatgggtttcgttttgtgtgaaaccaattccaattgtatcgtttagttcaattgattgattatgagttggtcaatgcagAAATTGGTTTTTACGGCGAGAAAGAATGGTACTTCTTTTCTCCTCGGGACCGGAAATACCCGAACGGTTCACGGCCGAACCGCGCCGCCGGAAGCGGCTA

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G24220.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------------------gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaa---ttgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
                                                                            ||| ||  ||    | |  ||      |||      ||    ||    |  |     ||||  |||   |   | | | |  || | ||||  | |||  ||   || ||||| |||||||| || ||| ||||| ||||||| ||||||||||||||   |||||||||| || | ||||| || |||||
gtaacagtaatacacaaatcgaatccattatctttttttctctcctctgcgactttttttcgttttccttctctgctaaccatcagatccaccttataattctgaaatatataatatttttttattaataaataattttattttcttttggtgtcgtgttat-gcagGAATGGCTTTGTACGGAGAGAAAGAGTGGTATTTTTTCACGCCGAGGGACCGCAAGTACCCGAACGGTTCGCGGCCGAACCGGTCCGCGGGAACCGGGTA

upper sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA06G11970.1 (Glycine max), 3'ss of exon 1
gtaagcaagagcaaaagcagatcgaatcgaatcgaggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
|||| ||  | ||       ||  | ||       |     |||     ||||   ||| | |||||||    | ||  | | || |||    ||| |     || ||||| |||||||||||||| || || ||||||||||| ||||| |||||   | |||||||| ||||||| || || || ||
gtaa-cataatcattcattcattcattcattcttcgatttctgattcttaatttttattta-ttaattgttactgtgttact-ttacagGATTGGCTACTTATGGAGAGAAAGAGTGGTACTTCTTTTCACCACGGGACCGGAAATACCCAAACGGTTCGAGGCCGAACCGGGCGGCTGGCACCGGTTA

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|87005047|gb|CI308923.1|CI308923
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
EST: gi|88327215|gb|CI652256.1|CI652256
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
EST: gi|88325801|gb|CI649636.1|CI649636
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
EST: gi|428011|gb|D24158.1|D24158
EST:     GGTGATCGCCGAGGTGGACCTNTACAAGTTCAACCCATGGGATCTTCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGT
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGT
EST: gi|86831929|gb|CI303369.1|CI303369
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
EST: gi|88729401|gb|CI752911.1|CI752911
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
EST: gi|88363116|gb|CI616273.1|CI616273
EST:     GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCG                         AGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC
genomic: GGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACC

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), 62 (downstream exon)
Score: 13

GTGATGTACTACCTGTGCCGCAAGTGCGGCGGCCTCCCCCTCGCCGCCCCGGTGATCGCCGAGGTGGACCTCTACAAGTTCAACCCATGGGATCTCCCCGgtaagcaaga ... attgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggaaattgaagtcgaattcaaattcaattaattggggatttggaattgttgcagAGAGGGCGATGGGAGGGGAGAAGGAGTGGTACTTCTTCTCGCCGCGGGACCGGAAGTACCCGAACGGGCAGCGGCCGAACAGGGCGGCGGGGACGGGGTA
                          aattaat  putative branch site (score: 13)
               aattcaaattcaatta  TA-rich tract