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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatcgatctgattgatcgatatttgtattcctggttactgaaactaattttcacagacacttgcattacatcgtgggagtgcaatgtaagagattaatggtggttttatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAGCAAGAGCTTCAAAGAACTCGGCAACAG

Basic information

species Physcomitrella patens
transcript PP1S126_196V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S126_196V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G36010.1 (Glycine max), 3'ss of exon 4
gtgatcgatctgattgatcgatatttgtattcctggttactgaaactaattttcacagacacttgcattacatcgtgggagtgcaatgtaagagattaatggtggttttatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAGCAAGAGCTTCAAAGAACTCGGCAACAG
                       |||| ||   |    | |||  |    | | |||  ||     ||||     | |   | | |   |  |  |   || || | ||   |||||||||||||||||||||||||| || |||||| | || ||||   || | |||||||| ||| || |  |  | || |||
----------------------gtttgaatgaatatgcattgattcgttgtctgacacgca-----attagtgtttagatatactaatgatcatgtggttgctgatattgccttacagGCCTATGTGCAGCAGTTAGAATCAAGTCGTTTGAAGTTGATGCAGTTGGAGCAAGAACTTGAACGTGCAAGACAGCAG

upper sequence: PP1S126_196V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G02430.3 (Glycine max), 3'ss of exon 4
gtgatcgatctgattgatcgatatttgtattcctggttactgaaactaattttcacagacacttgcattacatcgtgggagtgcaatgtaagagattaatggtggttttatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAGCAAGAGCTTCAAAGAACTCGGCAACAG
                       |||| ||   |      ||| ||  ||| ||| | |  |    | |   | |    | |    |  | | | ||  || |    ||   |||||||||||||||||||||||||| || |||||| | || ||||   || | |||||||||||| || |  |  | || |||
----------------------gtttgaatgaatatacgttgatac--attgtcagacatgcaattagtgtttagatatactaatgttcatgtggttgctgata---ttggcttacagGCCTATGTGCAGCAGTTAGAATCAAGTCGTTTGAAGTTGATGCAGTTGGAGCAAGAGCTTGAACGTGCAAGACAGCAG
















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|67573175|gb|BJ945999.1|BJ945999
EST:     GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAG                         GCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG
genomic: GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAGgtgatcgatc ... tatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG
EST: gi|100362435|gb|BY947355.1|BY947355
EST:     GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAG                         GCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG
genomic: GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAGgtgatcgatc ... tatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG
EST: gi|208372398|gb|DC936500.1|DC936500
EST:     GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAG                         GCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG
genomic: GTCTGGCACAAAATCGTGAAGCAGCCCGAAAAAGCAGGCTTAGGAAAAAGgtgatcgatc ... tatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcattacatcgtgggagtgcaatgtaagagattaatggtggttttatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAGCAAGAGCTTCAAAGAACTCGGCAACAG
                              gattaat  putative branch site (score: 3)
                                          ttttatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatcgatctgattgatcgatatttgtattcctggttactgaaactaattttcacagacacttgcattacatcgtgggagtgcaatgtaagagattaatggtggttttatgttacagGCCTATGTGCAGCAGTTAGAGTCCAGTCGTATCAAATTGAACGAGCTTGAGCAAGAGCTTCAAAGAACTCGGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC