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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatctttgaaacccgatcagtgcctaacaatgactgactgtatatgaagatgtacaaatgttttccgttgcataggattgtcaatttgaactgg...

Basic information

species Physcomitrella patens
transcript PP1S35_94V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 5'ss of exon 3
TGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgta-------atctttga--aacccgatcagtgcctaacaatgactgactgtatatgaagatgtacaaatgttttccgttgcataggattgtcaatttgaactgg
||||||||| |  |||||||| || |||||| |    ||||||||||| ||||||||||||||||||||||| ||  |||| ||  ||||| |  |  ||||  |||        ||||||    ||   || |   || ||  ||   |   ||| ||||  |   | | |||  | |    |   | |      || |||| |    
TGACCACGCAAGTAACCTGGCTACCAAAATTAGGAATAATCTCACCAATTCTATGAAGGCACTTGGTGTTGACATATTGACAGGGTTTGGCGCTGTTCTGgtcagtatgttattgtctttggttgactatataaactccaaatgataggtcgttgt-tatgtggtgatcctaatactctttagtcttttgtg----cactttgcag---
















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|162195483|gb|FC370900.1|FC370900
EST:     TGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: TGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
EST: gi|162167619|gb|FC343751.1|FC343751
EST:     CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
EST: gi|162166909|gb|FC343294.1|FC343294
EST:     CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
EST: gi|100420741|gb|BY993485.1|BY993485
EST:     CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
EST: gi|162170369|gb|FC346774.1|FC346774
EST:     CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
EST: gi|162189578|gb|FC365800.1|FC365800
EST:     CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTG                         GCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG
genomic: CTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTG

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), 24 (downstream exon)
Score: 7

TGACCACGCCAACAACCTGGCCACTAAAATTCGAGGAAATCTCACCAACTCTATGAAGGCACTTGGTGTTGATATTCTGACTGGTGTTGGCTCCATCGTGgtatgtaatc ... tttcttacagGCTCCTCAAGTTGTGAAATATGGAAAAATTGGATTTTCTGACAAAACTGTGACAGCACGCAACATTATCATTGCAACTGGTTCGGTGCCTTTTGTTCCTC




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