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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgtgagattctcaagtctttgcgttgtatagtatgaattgctgtccttatggaatgtctagtccaagacttttgcatgttctgtccagcctatcgtatcca...

Basic information

species Physcomitrella patens
transcript PP1S26_115V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 9
TGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgt-gagatt---ctcaagtctttgcgttgtatagtatgaattgctgtccttatggaatgtctagtccaagacttttgcatgttctgtccagcctatcgtatcca--------------------------
||||||||| ||||||||||| |||||||||||||| || ||||| || ||||| || |||   || || |   |   || | | |  | |    || |   | | |  | |||| |   |  ||| | | |  | |||  ||| |  |   | |                           
TGCTTTGGTCTGGGGTTCAAGTGCAAAACACAAGCCTCAAAGAGTTGGCAAGgttgatattgtacttaatttactttatttt-tggcttcatcctctttttgtgttgtgtttctacttttattcttctccctcat-tgttgagcatgccacctactaatcgaaatatgttgttgcttaccag

upper sequence: PP1S26_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 9
TGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgt-gagattctcaagtctttgcgttgtata--gtatgaattgctgtccttatggaatgtctagtccaagacttttgcatgttctgtccagcctatcgtatcca--------------------------
||||||||| ||||||||||| || ||||||||||| || ||||| || ||||| || | | |      ||| | || | |   |  | |    || | | ||| | || |||| |   |  ||| | | |  |  ||  | | | ||   | |                           
TGCTTTGGTCTGGGGTTCAAGTGCGAAACACAAGCCTCAAAGAGTTGGCAAGgttgatactgtacttaatttacattattttttgcttcatcctcttttcgtattgtatttctacttttattcttctccctcgta-gttgaacatgtcacctactaagtggaatatgttgttgcgtaccag

upper sequence: PP1S26_115V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT4G39520.1 (Arabidopsis thaliana), 5'ss of exon 9
TGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgtgagattctcaagtctttgcgttgta---tagtatgaattgctgtccttatggaatgtctagtccaa-gacttttgcatgttctgtccagcctatcgtatcca----
 ||| |||| ||||||||||| || |||||||||||||| ||||| |||||||| || |  || ||    |       |   || | ||       |   ||     ||  ||     |   ||| |||| |||   | | | | |||  ||| |     
CGCTCTGGTTTGGGGTTCAAGTGCCAAACACAAGCCACAAAGAGTTGGAAAGgttagttcttctagcaaatcaaacaaaagttaatctggtaaatcgatattgcaatatccctgactaactaactattgc-tgtctcgac-atcgtattttatacttcag

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|162190979|gb|FC368385.1|FC368385
EST:     CTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAG                         GAACATACTTTGGAGGACGAGGACGTTGTCCAGATTATTAAAAAAGTGTGA
genomic: CTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgtgagattct ... aatccttcagGAACATACTTTGGAGGACGAGGACGTTGTCCAGATTATTAAAAAAGTGTGA
EST: gi|67695517|gb|BJ955750.1|BJ955750
EST:     CTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAG                         GAACATACTTTGGAGGACGAGGACGTTGTCCAGATTATTAAAAAAGTGTGA
genomic: CTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgtgagattct ... aatccttcagGAACATACTTTGGAGGACGAGGACGTTGTCCAGATTATTAAAAAAGTGTGA

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: 32 (upstream exon), 35 (downstream exon)
Score: 16

TGCTTTGGTGTGGGGTTCAAGCGCAAAACACAAGCCACAGAGAGTGGGAAAGgtgagattct ... aatccttcagGAACATACTTTGGAGGACGAGGACGTTGTCCAGATTATTAAAAAAGTGTGACATCTTATGGCTGCTGAAGGATGGGTCATTCAATACTTGTTCGGTTCGT




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