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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggtaacattacaattctttattactgagtgttttctttttgtgatccatgataag

Basic information

species Oryza sativa
transcript LOC_Os08g17390.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G328908_T01 (Zea mays), 5'ss of exon 4
GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggtt-ctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggtaacattacaattctttattactgagtgttttctttttgtgatccatgataag
 ||||||||||| |||||||||||| |||||||||| || ||  | ||||||   |||||| | ||||| |  ||||||||||||||||| || ||||| ||||||  |  |  |  | | |    |  || | | | || ||   ||  |  |   | | |  ||   |  | | |   || ||  |||   ||||  |  |||   ||  |            
CAAGCCTCTGTTCGTGATCCCTCATGAGAAGCACAGAGATGAAATCGAGGAGGAGGTGGGGGACGACACAAGCATCCTGTTCATCACCACCCCAGGCCAGgtaggtggcgctactagtacatatacatgat-aatctccagtccagaatgaaatggaaccttaatttgaatatgaaacatcacttaattac--ctgaccgacttccaattaag------------

upper sequence: LOC_Os08g17390.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM5G838196_T02 (Zea mays), 5'ss of exon 4
GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctttgatgcttcttcattacaatcactttgcaatctgaaaacaccttagatcatctttcacaggta-acattacaattctttattactgagt-gttttctttttgtgatccatgataag
 ||||||||||| |||||||| ||| | |||||||| || ||||| ||||||   |||||| | ||||| || ||||||||||||||||| || || || |||||      | ||  || ||  | | |  || |   |||||  | || |   |||       |   |  |    ||   ||   |   ||||   |   ||||||    |    ||| |     
CAAGCCTCTGTTCGTGATCCCCCATGACAAGCACAGAGAGGAGGTCGAGGAGGAAGTGGGGGACGACACGAACATCCTGTTCATCACCACCCCAGGACAGgtaggcg----gttgtctcatctgttctagtacatgataatctccatacgctgcagaatggaaatggtacctctgaatctgaaagatggcttaccatgccattttctgaccgactcccaag-----
















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|86260747|gb|CI000195.1|CI000195
EST:     TCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCGACACCGCC
genomic: TCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|86254877|gb|CI016997.1|CI016997
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGGCCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|84117395|gb|CD151162.1|CD151162
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|88225708|gb|CI225624.1|CI225624
EST:     TCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: TCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|88219694|gb|CI219254.1|CI219254
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|33797795|gb|CF324757.1|CF324757
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|86501067|gb|CI143700.1|CI143700
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|86859484|gb|CI278882.1|CI278882
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|88974544|gb|CI022085.1|CI022085
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|38473524|gb|CF957656.1|CF957656
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|86499661|gb|CI142294.1|CI142294
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|87021778|gb|CI277945.1|CI277945
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
EST: gi|86504480|gb|CI147113.1|CI147113
EST:     AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAA                         CTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC
genomic: AGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCC

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: 64 (upstream exon), 45 (downstream exon)
Score: 13

GAAGCCTCTGTTTGTGATCCCTCATCAGAAGCACAGGGAAGAGGTTGAGGAGACTGTGGGGAAGGACACCAATATCCTGTTCATCACCACTCCTGGCCAAgtaggttctt ... ccatgataagCTCACCTGCCTCATCAACGACTCCGTCGGCGTCGTCGCGACCAACACCGCCGCCGTCCAGCTCGCCAACGCCAGGGACAAGCCATG




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