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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctgaattgtcctgctggcgtcttgatactggataatgctctttgaacatattcctaatcatcaattcttgttcgaggacgttattcaaacatgagtcggcatgtagtctgcctcactcttttgaactttcgtgcgattttacag

Basic information

species Physcomitrella patens
transcript PP1S49_154V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 3
AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctgaattgtcctgctggcgtcttgatactggataatgctctttgaacatattcctaatcatcaattcttgttcgaggacgttattcaaacatgagtcggcatgtagtctgcctcactcttttgaactttcgtgcgattttacag
 || ||    ||||| ||| | ||| || |   ||||||||||||||||||| | |||||||| || || ||||| |||   || ||||| ||||||||||| |||      || |||   |   |   |  || || || |      |||   ||| |  |  | |  |||  ||    | ||    |     ||  || ||       | |                                      
GGCTGCTCAGGAGGTTGCTGAAGGACAGTTAGATGACCACTTTCCACTTGTTATCTGGCAAACTGGGAGTGGCACACAAAGCAACATGAACGCCAATGAGgttttt------ttttcccatta-tgcactactattgtatgaa-----ttgtctatactgtttgttactaataattaaatgtggtacctgcc--aatgtgcgttaaagctttga-------------------------------------

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 3
AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctgaattgtcctgctggcgtcttgatactggataatgctctttgaacatattcctaatcatcaattcttgttcgaggacgttattcaaacatgagtcggcatgtagtctgcctcactcttttgaactttcgtgcgattttacag
 || ||    ||||| ||  |||||||| ||  ||| ||||| ||||||||| | |||||||| ||||| ||||| |||   || |||||||||||||||||    | ||   |   |  |     | ||  ||||  | |||  ||  | || | ||    |||  | || |  | |    |    || ||  ||    | ||                                               
GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTGGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgt---cggtgtcctacacacccaatatttt--tacttca-aatcttccataaaaacatc---aattttaaagtagtatagctgttttttttttgaatggcaatccctgc------------------------------------------

upper sequence: PP1S49_154V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G348729_T01 (Zea mays), 5'ss of exon 6
AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctgaattgtcctgctggcgtcttgatactggataatgctctttgaacatattcctaatcatc--aattcttgttcgaggacgttattcaaacatgagtcggcatgtagtctgcctcactcttttgaactttcgtgcgattttacag
 || ||    ||||| ||  |||||||| |   ||| ||||| ||||||||| | |||||||| ||||| ||||| |||   || |||||||||||||||||   || ||   |      |     | || |  |   ||  | |           |||   ||  |    |  | ||||| |     ||  | |   |   |                                                  
GGCAGCTGAGGAGGTCGCAGAGGGAAAGTTAGATGATCACTTCCCACTTGTTATCTGGCAAACTGGCAGTGGCACACAAAGCAACATGAATGCCAATGAGgt---tggtgtcctacatatccaatatttttactccaaatcttccataaaacgtcaattttaaagtagtatagctgttgtttggaatggtagtccctgctaaa--------------------------------------------------

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|208363600|gb|DC939777.1|DC939777
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|100377587|gb|BY986312.1|BY986312
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCA-G
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18351239|gb|BJ183291.1|BJ183291
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18365619|gb|BJ197696.1|BJ197696
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18372221|gb|BJ203823.1|BJ203823
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCA
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCA
EST: gi|18362649|gb|BJ194720.1|BJ194720
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTAT
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTAT
EST: gi|208358694|gb|DC942916.1|DC942916
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18372136|gb|BJ203738.1|BJ203738
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTAT
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTAT
EST: gi|18326303|gb|BJ158302.1|BJ158302
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCANT
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18343443|gb|BJ175481.1|BJ175481
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
EST: gi|18370151|gb|BJ201753.1|BJ201753
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCA
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCA
EST: gi|18364496|gb|BJ196569.1|BJ196569
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGNTGAGAT
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGAT
EST: gi|18366250|gb|BJ198328.1|BJ198328
EST:     TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAG                         GTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG
genomic: TTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAG

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: 34 (upstream exon), 34 (downstream exon)
Score: 15

AGCGGCCAGTGAGGTAGCTCAGGGAAAGCTGACTGACCACTTTCCACTTGTTGTTTGGCAAACGGGCAGCGGCACTCAATCGAATATGAATGCCAATGAGgtatttgctg ... gattttacagGTGATTGCTAATCGTGCGGGTGAGATTATCGGTATCCCTATTGGCAGCAAGGGGGTCCATCCCAACGATCACGTTAACATGAGTCAATCCTCAAATGACA




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