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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTCGTAGTTGTTATGATGAAGGAAAGCGTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccgaattttcatggattttgaatatgcagtggcagtagtttacggtaagttccatttaggaagtcatcgaaggctatggattagctggtggagttctaattcgagaaatcacaaaggtgttgttttgctgcaaggtttttgaggtttgaagtggtgcag

Basic information

species Physcomitrella patens
transcript PP1S209_52V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 3
GTGTTCGTAGTTGTTATGATGAAGGAAAGCGTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtaca-gtccgaattttcatggattttgaatatgcagtggcagtagtttacggtaagttccatttaggaagtcatcgaaggctatggattagctggtggagttctaattcgagaaatcacaaaggtgttgttttgctgcaaggtttttgaggtttgaagtggtgcag
|||   | ||||| ||||||||||||||||||||||| || || ||||| ||||| || ||| |||||||||  ||  ||||| |  | | ||| |  |   ||   || | |  | ||  ||   ||       || ||  |||| | ||   | | |   | ||||    ||  |      || ||||    |                                                    
GTGAGAGGAGTTGCTATGATGAAGGAAAGCGTACTGCAGAAACCCTGGCCATGGATTATCACCGAGGTGCAGGTGTGGAGgtaaatattctaatatctactcatg--gattgtatattgcaagctctt-------agctcactttatggagaacttgtacaatctgga---actcata---ccctcattcacaca----------------------------------------------------
















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|162196627|gb|FC374917.1|FC374917
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162207029|gb|FC383038.1|FC383038
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162261552|gb|FC437569.1|FC437569
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|67699664|gb|BJ959897.1|BJ959897
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|37852244|gb|BJ610252.1|BJ610252
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162194370|gb|FC371088.1|FC371088
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162193738|gb|FC371265.1|FC371265
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162155079|gb|FC330873.1|FC330873
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162181366|gb|FC358435.1|FC358435
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAAGTGCAGAAGTTCAA                         GTTCGCATTGCTCGTAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTAT
EST: gi|67695896|gb|BJ956129.1|BJ956129
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162155078|gb|FC330872.1|FC330872
EST:     AGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: AGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162245552|gb|FC424106.1|FC424106
EST:     GACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|37825569|gb|BJ583635.1|BJ583635
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
EST: gi|162193739|gb|FC371266.1|FC371266
EST:     GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAG                         GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT
genomic: GTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGAT

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: 35 (upstream exon), 35 (downstream exon)
Score: 26

GTGTTCGTAGTTGTTATGATGAAGGAAAGCGTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccg ... agtggtgcagGTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTCGTAGTTGTTATGATGAAGGAAAGCGTACTGCGGAGACACTGGCAATGGACTACCACAGAGGTGCAGAAGTTCAGgtacagtccgaattttcatggattttgaatatgcagtggcagtagtttacggtaagttccatttaggaagtcatcgaaggctatggattagctggtggagttctaattcgagaaatcacaaaggtgttgttttgctgcaaggtttttgaggtttgaagtggtgcag

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