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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcattattctttgcttgttttcacaagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG

Basic information

species Oryza sativa
transcript LOC_Os07g26610.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 16
gtatgtcattattctttgctt-gttttcac-aagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG
||||||   |||||||||||| ||| |  | ||  |||| |||| ||||||||  |  ||  |||||||  |  |   ||||||  |||||  ||  |   | |||  |||   |    || |||||||| ||||||||||||||||| ||||||||  || || | || || ||||| || ||||||||||| ||||| |||
gtatgtacatattctttgctttgttctttcgaaacttgaatatagatcttgatgca--taatttttcttctgcgagaaagctgga-tttctgcttatt---ttatggcataccat----acacagGTAAGGGTTTCAGGATATGGTGGGTGGTTCTTGCTGAGGCTCTCTCTGCATGATCCTGTTCTTCCCCTAAACATTGAG

upper sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 16
gtatgtcattattctttgcttgttttcacaagtttgagtatatatcttgatatatctaccttttcttgggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG
                                     ||   | | | |||||||      |  || |  |    |  ||   ||   |  |     | |         |||  |  |   || |  | ||||| || | |||||| |||||  |  |  |  | || |||||||| || |||||||||||||||||||||
-------------------------------------gtgagtgt-tagatatatgagggctccctagaatc---tgcctccactacatagtataaatctttcatctcttttgcaaaaaatagATCCGCGTTTCGGGCTTTGGTGGATGGTTTCTTCTCAGACTTTCTCTCCATGATCCTGTTCTTCCCCTTAACATCGAG
















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|89183519|gb|CI046084.1|CI046084
EST:     GAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: GAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86831683|gb|CI301533.1|CI301533
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86259591|gb|CI065464.1|CI065464
EST:     TGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGTTTATCCCTCCAT
genomic: TGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|218504169|gb|FG954519.1|FG954519
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|88268519|gb|CI378454.1|CI378454
EST:     AAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: AAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|87008287|gb|CI301045.1|CI301045
EST:     TAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: TAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|29660679|gb|CB656954.1|CB656954
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|89186475|gb|CI048147.1|CI048147
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86426061|gb|CI071158.1|CI071158
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86892585|gb|CI312008.1|CI312008
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
EST: gi|86258642|gb|CI064995.1|CI064995
EST:     CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGC                         GTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT
genomic: CAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCAT

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: 75 (upstream exon), 72 (downstream exon)
Score: 30

GTCCTTCCGTGATTACGGAGAAGCTGTCTTGAAACATTTGGAGAATGCAATCAGTAAAGATGAATATCTGTGCAAAGCACCGAAGAACTATGAAGGCgtatgtcatt ... tactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaaagtagctgggctttcttattgctgtatcatgctatatttttactacgcagGTAAGAGTTTCAGGATATGGTGGCTGGTTCTTATTGCGGTTATCCCTCCATGACCCAGTTCTTCCCCTTAACATCGAG
                                         tttttact  CT-rich tract
                                     tatatttttacta  TA-rich tract