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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaaaaatctcgcgatcttagaatgcgctattgatctctttccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA

Basic information

species Selaginella moellendorffii
transcript EFJ34798
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34798 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP03478 (Chlamydomonas reinhardtii), 3'ss of exon 2
---------------------------------------------gtagaaaaatctcgcgatcttagaatgcgc-tattgatctctttccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                                             ||        || |     ||   ||| |  ||  |  |||  | || | ||   |||||  ||   ||   |||||||||| |  ||||||||||||| || |||||||||||||||||     | || ||| | |||||||||||||| || ||||
gggcgcggcggcaaccgcgcgagcctgcgactgcttctggcctacgtccgtgtgacttggaggtttgtcatgagtgtaacgggctcggtgcattttg---cagGTGGTCGTCCGCGCCGAGGAGATTACCATCTCGGGCGGCCTGGTGCGCCAGAAGATGAAGTATGACCGCTTCCTGCGCAAGCGCATGAACACCAACCCCA

upper sequence: EFJ34798 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S165_40V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------------------------------------------------------gtagaaaaatctcgcgatcttagaatgcgcta-ttgat--ctctttccactgtgtt---ccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                                                                                                           ||||     |     | ||     |   |  | ||||    ||| ||  |||  |     |||||| |    || |  ||||| ||    || || || ||||||||  | ||||||||||||||| |||||||| |||||||| | |||||||| ||||| |
gtacgtactctgtacttttcttgtaatatatatatatatatatatatatatatatacatacttatatatatttgaagtatttttttttctctatgtgtgattctctcgtaggttgcttatttgttcgggagacatggaaattgaatgttctatctgctggttggggtcagGTTGTTGTTCGTTCTGAGGAAATCTGCCTGTCCGGTGGCCTCGTGAGGCAGAAGATGAAGTACTTGAGGTTTTTGAGGAAGAGGATGAACACTAAGCCTA

upper sequence: EFJ34798 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S75_223V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------gtaga---aaaatctcgcgatcttagaatgcgc---tattgatctctttccactgtgttc----cagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                                              ||| |    || ||   ||    | | || |||   | || || || |  |  | |||||    |||||| |    || |||||||||||     | || || ||||| ||  | ||||||||||| ||||| |||||| |||||||||| |||||||| || ||||
gtacgtcctcggtcacgcttatttccccgatttttcaactacctgtgtaaacttgaattcgttcgcctgtgggattcgcggattttcatatcctcgcttt-tgttcaaaccagGTTGTTGTACGTTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAGAAGATGAAATACCTAAGGTTTTTGAGGAAGCGGATGAACACCAAACCCA

upper sequence: EFJ34798 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S80_110V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------gtagaaaaatctcgcgatcttagaatgcgctattg-atctctt-tccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                        |   |   | |  |   | | |   | | || ||  | |||  |  | | ||  ||||||| ||   || | |||||||||    || || || || || ||| | ||||||||||| || ||||||||| |||||||| | |||||||| |||||||
gtaagtcctctattgccttttcgctctgagtttttttctcccgttgttagtgttactgtgtttctcatgtattttgaaccagGTTGTCGTCCGCTCCGAGGAGATCTGCCTGTCAGGTGGTCTTGTCAGGCAGAAGATGAAATATCTGAGGTTTTTGAGGAAGAGGATGAACACCAAGCCCA

upper sequence: EFJ34798 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S63_162V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------------------------gtagaaaaatctcgcgatcttagaatgcgctattgatctctttccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                                                                          |       | | |   |||  ||||    | | | || | |     ||  |  |||||  |    || |||||||||||     | || || ||||| ||  | ||||||||||| ||||| |||||| |||||||| | |||||||| |||||||
gtatgtactctgcctctgcaatgcgcgccttctcacatgttgtccgtttttttttttttttttttttttttttttccgtttctgtggaattctcggaatttaatgtag-tcacctggggttgaat--cagGTCGTTGTTCGCTGCGAGGAGATCTGCTTGTCAGGTGGCCTTGTGAGGCAGAAGATGAAATACCTTAGGTTTTTGAGGAAGAGGATGAACACCAAGCCCA

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|169100109|gb|FE501868.1|FE501868
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169094936|gb|FE491644.1|FE491644
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169050490|gb|FE459597.1|FE459597
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169044734|gb|FE454075.1|FE454075
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169033363|gb|FE441755.1|FE441755
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169047185|gb|FE457266.1|FE457266
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169033364|gb|FE441756.1|FE441756
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169036055|gb|FE446761.1|FE446761
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169063743|gb|FE472473.1|FE472473
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169050489|gb|FE459596.1|FE459596
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169100110|gb|FE501869.1|FE501869
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169063744|gb|FE472474.1|FE472474
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169023345|gb|FE431867.1|FE431867
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169078892|gb|FE489664.1|FE489664
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
EST: gi|169077600|gb|FE484862.1|FE484862
EST:     GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTG                         GTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG
genomic: GCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAG

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: 62

GGGAGCTTGCGCGCGGGTGGTGGTGATCGATGCGCGCCATCACATGCTTGGCCGGCTGGCCTCGATCGCCGCCAAGGAGCTCCTCAACGGACAGCGCCTGgtagaaaaat ... tgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaaaatctcgcgatcttagaatgcgctattgatctctttccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA
                            tattgat  putative branch site (score: 62)
                                  tctctttccactgt  CT-rich tract
                 ttagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaaaaatctcgcgatcttagaatgcgctattgatctctttccactgtgttccagGTTATCACGCGATGCGAGGAGATTGCTCTCTCGGGCGGCCTCGTCCGCCAGAAGATGAAGTACCTGAGGTTTCTGAGGAAGCGCATGAACACGAAGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG