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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgtttctgagatcctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT

Basic information

species Selaginella moellendorffii
transcript EFJ23913
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G01990.1 (Glycine max), 3'ss of exon 1
gtatgcgtttctgagat--cctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGA-----------------GGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
|||||  | |   |  |  ||  |||      ||  | ||| |   || | | || | ||| |   ||    |||  | | | |                 ||||| |||   ||  |||| ||||| || || ||||| || |||||||||||||| | ||||||||||||||||||||| || || |
gtatgtatataccaagttaccaactctcacattaccatgctatttgtgtttttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTGGTTGGAGGGTACTATGATGCTGGGGACAATGTGAAATTTGGTTTTCCCATGGCATTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT

upper sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA10G02130.1 (Glycine max), 3'ss of exon 1
gtatgcgtttctgagatcctgc----tcgt-tttataagaagctctacttgatctctttggttgttc-----tcttcaa----gGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
|||||| | |   |  ||   |     | | |||    |    | |  ||| | |  ||  || |       | | |||    ||| | | |    ||||| |||   ||  |||| ||||| ||||| ||||| || |||||||| ||||| | ||||||||||||||||||||| || || |
gtatgcatataccaactctcacattaccatgttttctggtttttgtttttggtttgcttatttatgtgtgaatgtgcaatgcagGTTGATTTAGTTGGAGGGTACTATGATGCTGGGGACAATGTAAAATTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCATGGAGCGTTATTGAGT

upper sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA03G37420.1 (Glycine max), 3'ss of exon 1
------------------------------------gtatgcgtttctgagatcctgctcgttttataagaagctctacttgatct--ctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
                                    || |  || || |   |  || ||  |   |      |    |||  |    | |||  ||| |  | || | || ||      ||||| |||   ||  |||| ||||| || |||||||| || |||||||| ||||| | |||||||||||| ||||| || || || |
gtatgataatataataatattaatacaacattcttagtctcagtctcagtttttgtgttctctggcttgtgcacatggcttatttctgcattgaatgtacaatgcagGTTGATTTGGTT-GGAGGGTACTATGATGCTGGGGACAATGTCAAGTTTGGTTTTCCCATGGCCTTCACCACCACCATGCTTTCGTGGAGTGTTATTGAGT

upper sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AT1G02800.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------gtatgcgtttctgagatc---ctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
                           |  |        || |      | |   |||| |  |||   ||| ||  | |   | | | |  | ||  |||||| | |    ||||| |||  |||  | || |||||  | |||||||||||||| ||||||||||| | ||| ||||| ||||||||  | || || |
accctaattttgttattatgctttttaggttaaaacagagaaactaagttacatattttcttggaaagcctaatttgtgtgaattggtttaattttgtagGTGGATTTGGTGGGAGGATACTACGATGCAGGGGACAATATGAAGTTTGGATTCCCAATGGCATTCACAACCACAATGCTCTCATGGAGTTTAATTGAGT

upper sequence: EFJ23913 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv07s0005g00740.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------------gtatgcgtttctgagatcctgctcgttttataagaagctctacttgatctc--tttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
                                  | | | | | ||||  | |   ||||  |    | | |  || || |     |||   |     |  |||||| | |    ||||| |||   ||| | || ||||| || |||||||| ||||| ||||| ||||| | |||||||||||||||||| ||||| || |
gtatgtgtaaatgtgtatgctctgtttcttcaattacttgttttagatttttcatcttttgaagttggttttg-ttaatttgggcgtggaaatggaaatgcagGTGGATTTGGTTGGAGGGTACTATGACGCAGGGGACAATGTGAAGTTTGGGTTCCCAATGGCCTTCACCACCACCATGCTTTCATGGAGTGTGATCGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT
                          acttgat  putative branch site (score: 5)
                                         ttgttctcttc  putative PPT
          ttttataagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcgtttctgagatcctgctcgttttataagaagctctacttgatctctttggttgttctcttcaagGTGGTTCTCCGAGGAGGCTACGTCGACTCTGGAGACAACGTAAAGTTTGGATTCCCCATGGCATTCACGATCACCATGCTTTCATGGAGCGTGATAGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA