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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG

Basic information

species Selaginella moellendorffii
transcript EFJ28600
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g21060.1 (Oryza sativa), 3'ss of exon 2
--cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtct-tgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG--
     ||  ||     | ||  || |  |   |  |||  ||    | || || | |   |  |     ||  || |    |   | | ||||||| | | |||| || |||||||| ||||||||||| ||||||||||||||    || |    || |  ||  | | || || |  || ||| |||||| | ||     |  
tgaaattaatcccttctatttttgat--actcttaatttcttaatcatatagtatatgcatccgtgtgattgatcgatcgatgtgcgtggatttttgtgc-agCTGGATGACTGGGTGCTGTGCCGGATCTACAAGAAGAGCAGCCACGCGTCGCCGCTG--GCCGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCGTGCG

upper sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G430849_T01 (Zea mays), 3'ss of exon 3
--cgtttcttcta-gagttttcatggtgaatcat--cgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG-----
   | |   | || | |||  ||  |     |||  || |     |||  |||   || |  |    |  || | | |  ||  |    ||| | ||   | ||||| ||||||||||| ||||||||||| |||||||||  | |    || |    ||||||| |  |  || || |  || | | ||||| |  ||   |       
atagctggctgtacgcgttgacagcgacggccatgacggtgacgacgac-gataacgtttcct----tgtttgcatgcccttgctggtgtcgttgttgcgtgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAAGAAGTCCGGCCACGCGTC---GCCGATGGTGCC--GCCGCTCGCCGACTACGAGCACCTCGACCGCGACGGAC

upper sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G011598_T01 (Zea mays), 3'ss of exon 2
-cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattt--tttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATG----CTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG
   | | | |  ||  | || |  |   |    | ||  || | | ||| |  | || |  | || | |   |  ||     |    | | |  |   | ||||| ||||||||||| ||||||||||| |||||||||  |||  |     |   | |||||    |  | | ||||| |  || ||| || ||| | ||      
atatatatgcatgatatatcctcttc--ttcctggtttatttgtgcgatggattattatt-gatcgtctgcgcgcgtacgcgtgcgtggtgtggtgcgtgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAAGAAGGCCAGCTGCCAGGTGCCGGCGATGGCGGCGGTGCCGCAGCTCTCCGACCACGACCAGGACGAGC----

upper sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgatttt----ttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATG-CTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG--
|| || ||      | | |||   ||    |  |   ||  ||    |   ||||    |  || | | | | | | | ||   || || |     |  | ||||| ||||||||||| ||||||||||| |||||||||  |||    |       ||||||| |  | | || || |  || ||| |||||| | ||   | |  
cgattgttgatccatctgcatc-cgatctgtgtagcatt--gattattttagtctccacatatcctct-tccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCC---GCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG

upper sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv00s0375g00040.t01 (Vitis vinifera), 3'ss of exon 2
cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAG-TGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG
             || |  ||||  |    |  ||   | |   || | ||    | | | |  |||      || | ||    | | | | ||    |||| ||||| ||||| |||||||||||||||||||||| ||  |     |  | |   ||      |  | || |   |    |||  | || || |  || 
-------------gtatatatggata--tgttaata--tgcattagtttgtagtctcttatggtattgaaaaaagctcttaat-ttgttgtgttggatagCTTGACGATTGGGTGCTGTGCCGGATTTACAAGAAGAACATCTCACAAAGGCCAATGGAGAGGGACAAGGAGGAGTCCATGGAGGCCCTGCTTGCATCCC-

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|169025896|gb|FE434417.1|FE434417
EST:     CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGG                         CTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC
genomic: CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaa ... ttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC
EST: gi|169024416|gb|FE436226.1|FE436226
EST:     CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGG                         CTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC
genomic: CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaa ... ttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC
EST: gi|169076128|gb|FE484430.1|FE484430
EST:     CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGG                         CTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC
genomic: CCAAGGCCGCCGCAGCGATTCCGGCCATGCGCAAGAAAGGATCGCTCAGGgtaagaagaa ... ttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG
                              tttttctcatcgattt  CT-rich tract
                                          atttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATGCTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
-gtttctt
- - - - - - - ttttcat
- - - - - - - - - - - - - - - - -attcttt
- - - - - - - - - - - - - - - - - - - - - -gagatcg
- - - - - - - - - - - - - - - - - - - - - - - - - tgtcttg