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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgtcttcgctccttcttcctccacgattttgacactctgttcgtttgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT

Basic information

species Selaginella moellendorffii
transcript EFJ25863
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25863 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 3'ss of exon 3
-gtaagtttgtcttcgctccttcttcc--tccacgattttgacactct----gttcgtt-tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT
  ||  |||    | | |  | ||| |  | ||  |||        ||    ||  ||| ||  |  |||||||| || || ||||| ||||||||| ||||||| ||| |||| |||||||| ||||| ||||| |||| ||| |||||||||||||| ||||| ||||
gttagatttcaacttgattgtacttgcatttcatcattgcagagaactaaaagtaggttatgcttttcagTGCCGACTCCATGAGCTCGCGAACAAGCGGAGGATCTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGT
















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|70669750|gb|DN838327.1|DN838327
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|70670787|gb|DN839364.1|DN839364
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169066324|gb|FE473000.1|FE473000
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169047645|gb|FE454813.1|FE454813
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169066323|gb|FE472999.1|FE472999
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169062114|gb|FE469173.1|FE469173
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169053896|gb|FE460987.1|FE460987
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|70669328|gb|DN837905.1|DN837905
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169062115|gb|FE469174.1|FE469174
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169019358|gb|FE427668.1|FE427668
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169106278|gb|FE507992.1|FE507992
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTTGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169019357|gb|FE427667.1|FE427667
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
EST: gi|169047646|gb|FE454814.1|FE454814
EST:     CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGG                         TGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT
genomic: CTGGGGGTGCGGCCGATTGTCAGTTCTGGCAGAGAAATCTCGGAACGCGGgtaagtttgt ... tgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcttcgctccttcttcctccacgattttgacactctgttcgtttgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT
                          ttttgac  putative branch site (score: 3)
                                       ttcgttt  putative PPT
                         attttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgtcttcgctccttcttcctccacgattttgacactctgttcgtttgaatcacagTGCCGGCTTCACGAGCTTGCGAACAAGAGGAGGATTTCTGTTGCCGGTGCTTCCAAGCTCTTGGCAAACACCCTCTACTCCTACCGTGGCATGGGTCTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT