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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCACTTGGTGGCACTACATTCAAGATGAAATTCGGTCATCATGGTGGAAACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattttcaaccacgctctatctccttgcttttgcaaatacatgctggcagtgtgcaagatcatctggtatagagttctaactaggctcaaaaaga...

Basic information

species Physcomitrella patens
transcript PP1S11_3V6.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S11_3V6.1 (Physcomitrella patens), 5'ss of exon 8
lower sequence: AT3G27740.1 (Arabidopsis thaliana), 5'ss of exon 8
GGCACTTGGTGGCACTACATTCAAGATGAAATTCGGTCATCATGGTGGAAACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattttcaaccacgctctatctc-cttgcttttgcaaatacatgctggcagtgtgcaagatcatctg-gtatagagttctaactaggctcaaaaaga------------------------------------------------------------------------------------
 ||  | || || |  || ||||||||||| || ||||||||||| |||||||| ||||| ||  |       || || |  ||||| ||||||||||||||    ||   ||||| |    | |  |  ||  ||      |||| | |   |   |     || | ||    |  | |||||  |  |   ||  | | |                                                                                    
AGCTTTGGGGGGTAAAACCTTCAAGATGAAGTTTGGTCATCATGGAGGAAACCACCCAGTTCGTAACAACAGAACTGGTCAGGTGGAGATCAGTGCTCAGgtaccaatacccaacctcaaaatgttccatttaattccaagcatac-taccaactaaggatttgaacttccacattcaaagttcggataattatctgataaaacgactgtgctaggaacattgttacaagcttgacaaaatctaaatatggtgtatcattgtctttttttctgtaattcttggcag
















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|37821875|gb|BJ579941.1|BJ579941
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
EST: gi|162257704|gb|FC433631.1|FC433631
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
EST: gi|162257705|gb|FC433632.1|FC433632
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCCACA-TTATGCAGTAGATCCCGATACATT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACC-ACAATTATGCAGTAGATCCCGATACATT
EST: gi|37824905|gb|BJ582971.1|BJ582971
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
EST: gi|37850684|gb|BJ608692.1|BJ608692
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
EST: gi|37825375|gb|BJ583441.1|BJ583441
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
EST: gi|37835533|gb|BJ593545.1|BJ593545
EST:     ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAG                         AACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT
genomic: ACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTT

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: 23 (upstream exon), 25 (downstream exon)
Score: 5

GGCACTTGGTGGCACTACATTCAAGATGAAATTCGGTCATCATGGTGGAAACCATCCAGTGCGCCATTTGCCCACCGGGCGCGTGGAAATCAGTGCTCAGgtcatcattt ... ttgaatgcagAACCACAATTATGCAGTAGATCCCGATACATTGCCGGAGGGTGTGGAGGTTACCCACATCAACTTGAATGATGGTACCTGTGCTGGCCTTACATTCCCTG




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