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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgtatatatatatatatatatatatatgcatcatcacctatctatctagcaatttactgaccatcgatcaatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG

Basic information

species Oryza sativa
transcript LOC_Os01g02120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059358_T03 (Zea mays), 3'ss of exon 1
gtatctgtatatatatatatatatatatatatgcatcatcacctatctatctagcaatttactgaccatcgatcaatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG--------------------------------------
               |||||||||      |    || |   | |||| |    | | ||      ||| |||  |||      || ||    || || | |||||||||||||||||| || || |||||||| ||||||||  ||||||||||||  ||||||||                                      
--------------gtatatatatgctggcacttgtc-tgctcgatctgtgcctccagttgacatgcatggatggattgcacaacttgct---gcgtg-tcgcagATCATGACGGACCCAGATGCGCCTAGCCCCAGCGACCCGACCATGAGGGAGTACCTCCACTGGTATGAACTGCTACAGCATGCTACGTACTTGTGTCATG

upper sequence: LOC_Os01g02120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G021614_T01 (Zea mays), 3'ss of exon 1
gtatctgtat-atatatatatatatatat-atatgcatcatcacctatctatctagcaatttactgac--catcgat-caatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG
|||  |     ||  || |   |  || |        | ||   ||  ||    |    | ||  ||   | ||| | ||| ||||| ||  ||   |   |  | |||||||||||||||||| || || |||||||| ||| ||||  ||||||||||||  ||||||||
gtacgtacgccatgcatgtcgttcgatcttgggcttcttattttcttgctgatgatgtgtgtatcgatgtcgtcgctgcaacttgct-gcatgcgtgcatgtcgtcgcagATCATGACGGACCCCGATGCGCCTAGCCCCAGCAACCCGACCATGAGGGAGTACCTCCACTG

upper sequence: LOC_Os01g02120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G059358_T01 (Zea mays), 3'ss of exon 1
gtatctgtatatatatatatatatatatatatgcatcatcacctatctatctagcaatttactgaccatcgatcaatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG
               |||||||||      |    || |   | |||| |    | | ||      ||| |||  |||      || ||    || || | |||||||||||||||||| || || |||||||| ||||||||  ||||||||||||  ||||||||
--------------gtatatatatgctggcacttgtc-tgctcgatctgtgcctccagttgacatgcatggatggattgcacaacttgct---gcgtg-tcgcagATCATGACGGACCCAGATGCGCCTAGCCCCAGCGACCCGACCATGAGGGAGTACCTCCACTG

upper sequence: LOC_Os01g02120.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT1G18100.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatctgtatatatatatatatatatatatatgcatcatcac-ctatctatctagcaattt-actgaccatcgatcaatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG
  |    || |  | ||  ||  ||| |      | |  |    |   | | | ||||||| | || || |   | |||  ||        | | ||||||    || | ||||| |||||||||||||||||||| ||||| ||   |||||| || |   |||||||
acaaaaata-acgtttaattagttatctgagctaaccgacgtgttgcatgtgttgcaatttcattggccgtatgtgaat--gcaaatatttcgatgcatgc----agGTGATGACTGACCCGGACGCACCTAGCCCAAGCGAGCCGAACATGAGAGAATGGGTCCACTG

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|218495548|gb|FG956083.1|FG956083
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218495786|gb|FG965856.1|FG965856
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218479392|gb|FG964734.1|FG964734
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|88585362|gb|CI702989.1|CI702989
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218487396|gb|FG969251.1|FG969251
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCGTCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|66914461|gb|CX101309.1|CX101309
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218499952|gb|FG964309.1|FG964309
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGC-ACGACCTCTAC-CCCTG                         ATC-TGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218486167|gb|FG951231.1|FG951231
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218495072|gb|FG958772.1|FG958772
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|88584026|gb|CI701549.1|CI701549
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGAACTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|88388601|gb|CI683383.1|CI683383
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTACCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|88592180|gb|CI710265.1|CI710265
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218484094|gb|FG956003.1|FG956003
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218483444|gb|FG953420.1|FG953420
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218482064|gb|FG957113.1|FG957113
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|88352680|gb|CI678699.1|CI678699
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218479589|gb|FG967768.1|FG967768
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218491779|gb|FG963455.1|FG963455
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218490459|gb|FG959442.1|FG959442
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGGCGCAACGACCTCTACAGCCTG                         ATCATGAGGGACCCGGACGCAGCTAGCCCTAGCGAACCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218493478|gb|FG952537.1|FG952537
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
EST: gi|218479879|gb|FG966076.1|FG966076
EST:     ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTG                         ATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG
genomic: ACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAG

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), 29 (downstream exon)
Score: 4

CGACAGGGACATCAGCAACGGCTGCCTCGTCCGCCCATCCGCCGCCGACTACCCTCCCCTCGTCCGCATCTCCGGCCGCCGCAACGACCTCTACACCCTGgtatctgtat ... atgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcaatttactgaccatcgatcaatttgctcgctcgccaacgcatgcttgcagATCATGACGGACCCGGACGCACCTAGCCCTAGCGACCCATCCATGAGGGAGTTTCTCCACTG
         tactgac  putative branch site (score: 4)
     aatttact  TA-rich tract