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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttattcaagtcttattttgggttcaaccctcaaattcatacagcaaaggaccatgagatcataatatatccatcgatgggccctggagctgaattatccttttaaactcctgcctttgtgaaaacctcatcacctctgatttctttggactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCCTACTTTGAGTCATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCC

Basic information

species Physcomitrella patens
transcript PP1S61_292V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_292V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ15497 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcttattcaagtcttattttgggttcaaccctcaaattcatacagcaaaggaccatgagatcataatatatccatcgatgggccctggagctgaattatccttttaaactcctgcctttgtgaaaacctcatcacctctgatttctttggactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCCTACTTTGAGTCATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCC
                                                                                  || |  || | ||| |||            |||  || | | |      ||||    |||| |    | ||   |   ||||| ||||||||||| ||||| || ||||||||  | || |||  |||||| ||||||||| | || ||||||||||||| |||||| || ||||| || |
---------------------------------------------------------------------------------gtgagtgctagcgctcaatct----------ctctcgcttctct------ctcactctctcttacgcttgtg---tctccagGTTTCCGAGAAGAAAGCCAAGGCCTGGTGTGCTTCCAAGGGAAACATCCCATACTTTGAGACGTCTGCCAAGGAAGACTACAACGTAGAGGCTGCCTTTC

upper sequence: PP1S61_292V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ24755 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcttattcaagtcttattttgggttcaaccctcaaattcatacagcaaaggaccatgagatcataatatatccatcgatgggccctggagctgaattatc-cttttaaactcctgcctttgtgaaaacctcatcacctctgatttctttggactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCCTACTTTGAGTCATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCC
                                                                                               ||| |  |  |  | || |||   |  || |      ||||    |||| |    | ||   |   ||||| ||||||||||| ||||| || ||||||||  | || |||  |||||| ||||||||| | || ||||||||||||| |||||| || ||||| || |
----------------------------------------------------------------------------------------------gtgagtgctagccctcaatctctctcgcttctc----tctcactctctcttacgcttgtg---tctccagGTTTCCGAGAAGAAAGCCAAGGCCTGGTGTGCTTCCAAGGGAAACATCCCATACTTTGAGACGTCTGCCAAGGAAGACTACAACGTAGAGGCTGCCTTTC
















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|162233790|gb|FC410056.1|FC410056
EST:     TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTG                         GTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
genomic: TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTGgtaagcttat ... gactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
EST: gi|208397058|gb|DC928901.1|DC928901
EST:     TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTG                         GTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
genomic: TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTGgtaagcttat ... gactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
EST: gi|162151879|gb|FC328125.1|FC328125
EST:     TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTG                         GTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
genomic: TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTGgtaagcttat ... gactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
EST: gi|208370838|gb|DC948291.1|DC948291
EST:     TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTG                         GTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
genomic: TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTGgtaagcttat ... gactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
EST: gi|208362282|gb|DC954528.1|DC954528
EST:     TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTG                         GTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC
genomic: TTGTAGTACTTGGAAATAAAGTGGACGTGGATGGTGGCAATAGTCGAGTGgtaagcttat ... gactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaactcctgcctttgtgaaaacctcatcacctctgatttctttggactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCCTACTTTGAGTCATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCC
                               ctctgat  putative branch site (score: 4)
                                    atttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttattcaagtcttattttgggttcaaccctcaaattcatacagcaaaggaccatgagatcataatatatccatcgatgggccctggagctgaattatccttttaaactcctgcctttgtgaaaacctcatcacctctgatttctttggactgcacagGTCTCCGAGAAGAAGGCCAAAGCATGGTGTGCAGCGAAAGGAGGCATCCCCTACTTTGAGTCATCAGCCAAGGAAGACTTCAACGTGGATGCTGCATTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC