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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgttattttctctgattttcttaaatccgaggtcatgtttttgcttacacatgttttgacgtacaatatttctctacagtactaaagtaaacacacttgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGTGGTTCTGTTACAGCTGGCAATGCTTCAAGTATCAG

Basic information

species Physcomitrella patens
transcript PP1S160_44V6.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S160_44V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA14G00760.2 (Glycine max), 3'ss of exon 5
gttcgttattttctctgattttcttaaatccgaggtcatgtttttgcttacacatgttttgacgtacaatatttctctacagtactaaagtaaacacacttgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGTGGTTCTGTTACAGCTGGCAATGCTTCAAGTATCAG
        || |  ||| | || ||    |    |||||  ||||  |   || |    |    ||||| ||   | ||  ||  ||   |   |    |  |||  ||||| ||||| |  || ||  | |||||||| |||   || ||      ||| |||||||||||||||||||||||||| || || ||
------acttctagctgctattattgttactatagtcattatttttgtcttactttcagttgaatacaa-ataaatatattgttatatttt---ccttttcctatgccagTTTGATGCTGCCAAGTTACGCAAACTTCGGCCAAGTTTCAAGGAGACTGGAGGTTCTGTTACAGCTGGCAATGCTTCCAGCATAAG
















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|100384912|gb|BY969647.1|BY969647
EST:     AGAG-CAAANCCATCCNATTTTTGT-GATAAAGATGATGGAATCGATAAG                         TTGGATGCNGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGAATGG
genomic: -GAGGCAAA-CCATCC-ATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGA-TGG
EST: gi|162258773|gb|FC434572.1|FC434572
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208372747|gb|DC952634.1|DC952634
EST:     GAAGAGGC-AACCATCCA-TTTTGNTGATAAAGATGATGGAATCGATAAG                         -TGGATGC-GGGAAA-TGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208364951|gb|DC947093.1|DC947093
EST:     GCAAACCATCCA-TTTTGNTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGG-AANTGAGAAAACTTCGACCAGCA-TTNAATCAGATGGT
genomic: GCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|22132646|gb|BQ827270.1|BQ827270
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|67727140|gb|BJ977399.1|BJ977399
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|162177571|gb|FC352429.1|FC352429
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208367940|gb|DC955375.1|DC955375
EST:     TTTG-TGATAAAGATGA-NGAATCGATAAG                         -TGGATGCGGGG-AANTGAG-AAACNTCGACCAGCA-TTAAATCAGATGGT
genomic: TTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|40781593|gb|AJ583523.1|AJ583523
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208362110|gb|DC943523.1|DC943523
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208353436|gb|DC922490.1|DC922490
EST:     AACCNTCCA-TTTTGTTGAT-AAGATGA-NGAATCGATAAG                         -TGGATGCGGGG-AATTGAGAAAACTTCGACCAGCATTT-AATCAGATGGT
genomic: AACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208389390|gb|DC953228.1|DC953228
EST:     TTTG-TGATAAAGATGATGG-ATCGATNAG                         -TGGATGC-GGGAAA-TGAG-AAACNTCGACCAGCATTTAAATCAGATGGT
genomic: TTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|208385682|gb|DC952843.1|DC952843
EST:     TTTTG-TGATAAAGATGA-NGAATCGATAAG                         -TGGATGCGGGGAAA-TGAGAAAACTTCGACCAGCA-TTAAATCAGATGGT
genomic: TTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|162166659|gb|FC343551.1|FC343551
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|19782978|gb|BQ039945.1|BQ039945
EST:     GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
genomic: GAAGAGGCAAACCATCCATTTTTGTTGATAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT
EST: gi|162177570|gb|FC352428.1|FC352428
EST:     TAAAGATGAGGGAATCGATAAG                         TTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCA-TTAAATCAGATGGT
genomic: TAAAGATGATGGAATCGATAAGgttcgttatt ... tgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttgacgtacaatatttctctacagtactaaagtaaacacacttgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGTGGTTCTGTTACAGCTGGCAATGCTTCAAGTATCAG
                           tactaaa  putative branch site (score: 1)
         tacaatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgttattttctctgattttcttaaatccgaggtcatgtttttgcttacacatgttttgacgtacaatatttctctacagtactaaagtaaacacacttgtattgcagTTGGATGCGGGGAAATTGAGAAAACTTCGACCAGCATTTAAATCAGATGGTGGTTCTGTTACAGCTGGCAATGCTTCAAGTATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG