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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagttgtttattttcttctgcttttctattcttccttttgcaagacaagatcttaaaaggcttctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA

Basic information

species Selaginella moellendorffii
transcript EFJ26216
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26216 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: EDO96600 (Chlamydomonas reinhardtii), 3'ss of exon 7
----------------------------------------------gcaagttgtttattt-tcttctgcttttctattcttccttttgcaagacaagatcttaaaaggcttctacttc---cagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA
                                              || ||     | ||   |  | |  |  |   | ||     |||       || ||  |     | |||||     ||||| || || |||||||| || || |||||||| ||||||   || ||||| || |||||||| |||||||| |||||||||||||| || ||||||||||
gtgcgtgtgctggacgcacgggtggggtgacggcccgggttcggaggccagccaagtgttggccagccgggtgccagcttttggggctgccgcgttcgacctgcatgtcttactactctatgcagGCGTTCGCCGACGAGATCGGCATTCCGTTCCTTGAAACCTCGGCGAAGAACGCCACCAACGTCGAGCAGGCGTTCATGACCATGGCCGCTGAGATCAAGA

upper sequence: EFJ26216 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S91_243V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------gcaagttgtttattttctt--ctgcttttctattcttcctt-----ttgcaagacaagatcttaaaaggcttctacttc----cagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA
              |   | ||| |||||  ||    |    || |  | ||  |     | |  ||  |    ||||   |     || ||     ||||| ||||| || ||||| ||||| || ||| ||||||| ||||| |||||||| |||||||| ||||| || |||||||||||||| || ||||||||||
atgggagttacttggtttgatgtctatttcgttgatggaggctcgacacctctgtagttgtggagaggtagaggcttatcggttcgttatttttgggcagGCATTTGCCGATGAGATTGGAATTCCTTTCTTAGAAACAAGTGCAAAGAATGCTACCAACGTGGAGCAAGCTTTCATGACCATGGCAGCTGAGATCAAGA

upper sequence: EFJ26216 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S95_20V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------gcaag-ttgtttattttcttctgcttttctattcttccttttgcaagacaagatcttaaaaggct---tctacttcc--------agGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA
              ||   |||  |||  |  |  |  ||  |||  |||     |      || | |    |   ||   ||||  | |        |||||||||| || ||||| ||||| || ||| | ||||| || |||||||||||||| ||||| |||||||| || ||||| |||||||| ||||| || |
ttgttcatttatttcagtcttggctatagttattcgacttcatatatttcacgcgggtgtggaaaaccccttaccactttatctatcttccatggagcagGCTTTTGCTGATGAGATTGGAATTCCCTTCTTGGAAACTAGCGCCAAGAATGCGACTAACGTGGAGCAGGCTTTTATGACAATGGCTGCCGAGATTAAAA

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|169031786|gb|FE438471.1|FE438471
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169057437|gb|FE465741.1|FE465741
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169046956|gb|FE455074.1|FE455074
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTTGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169056895|gb|FE465446.1|FE465446
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169107992|gb|FE511520.1|FE511520
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169057438|gb|FE465742.1|FE465742
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169061955|gb|FE469118.1|FE469118
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169046957|gb|FE455075.1|FE455075
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169061402|gb|FE470957.1|FE470957
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169074721|gb|FE481224.1|FE481224
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169061416|gb|FE470958.1|FE470958
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|70669218|gb|DN837795.1|DN837795
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|70671069|gb|DN839646.1|DN839646
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169112941|gb|FE515421.1|FE515421
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169056881|gb|FE465445.1|FE465445
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169031759|gb|FE438470.1|FE438470
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169034293|gb|FE443066.1|FE443066
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
EST: gi|169034294|gb|FE443067.1|FE443067
EST:     ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAG                         GCTTTCGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT
genomic: ACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAAT

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: 60

CGAGATCGATCGCTACGCGAGCGAGAATGTGAACAAGCTCCTCGTCGGTAACAAGGCCGATCTCACGGCCAAGAAGGTCGTCGACACCCAGACTGCCAAGgcaagttgtt ... ctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttttctattcttccttttgcaagacaagatcttaaaaggcttctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA
                                          cttctacttcc  CT-rich tract
                               atcttaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagttgtttattttcttctgcttttctattcttccttttgcaagacaagatcttaaaaggcttctacttccagGCTTTTGCAGACGAGATAGGAATCCCGTTCCTAGAAACCAGTGCCAAGAATGCGACCAACGTAGAGCAGGCATTCATGACCATGGCTGCGGAGATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA