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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacccctggtctggtctcactcttactgccgtgattcgaacgcgcgtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttctctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC

Basic information

species Selaginella moellendorffii
transcript EFJ32208
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32208 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os04g05050.1 (Oryza sativa), 3'ss of exon 3
---------aacccctggtctggtctcactcttactgccgtgattcgaacgcgcgtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttct---ctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC
         || |      |||  | |  ||||  |    |||||   |  |  |   |  ||      | |   |  ||    | ||   ||  ||  |          |   ||||  ||||    |||||| |   |  ||  ||   | ||       ||| ||||||||||||||||||||||||| | ||||||||  ||||||||
tcgtaattaaaactgaaaactgaacacgatcttggt----tgatt--gattcatgatgtgattaaaagataatggagttttttttaacaatggaattcatcatcagGTCGATCAGGAACAGCACGGCGAGGAGGAAGCTGGGCTACCTGTCGTGC------GGCACCGGCAATCCGATCGACGACTGCTGGAGGTGCGACCCGGACTGGCAC

upper sequence: EFJ32208 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G131912_T02 (Zea mays), 3'ss of exon 3
---aacccctggtctggtctcactcttactgccgtgattcgaac-gcgcgtcctc-tttgtcctttgaaaaaaatt-cgactcactccgggctttttttctctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC
   | |   |  | ||   |  ||| |  |  | |  |  |    |   || ||  ||| |  | | ||   | ||   | | | |      |  |       ||   ||||  ||||     || |  |      ||||       |  ||| | | |  ||||| ||||||||||||||||||||||||||| |  ||||||||
tgcatcaattactttgtgattgctccttttttcttcttctgtgtagttagtactagtttctagtataaatcgagttgttaataattggaatgtcgtgcagGTCCATCAGGAACAGCACGGCCCGGCGAAA-----CCTCGGGTACCTGTCGTG-CGGGACAGGCAACCCGATCGACGACTGCTGGCGCTGCGACTCGGACTGGCAC

upper sequence: EFJ32208 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G412207_T04 (Zea mays), 3'ss of exon 3
aacccctggtctggtctcactctta-ctgccgtgattcgaacgcgcgtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttctct-cagAGGGAATGGCA-CACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC
   || |  |   || |   |  ||  | |    | ||||      | |     ||          ||| |  || | |||    |  |   | |||| |||    |    || ||  | ||   |  |   |||||       |  ||| | | |  ||||| || |||||||||||||||||||||||| |  ||||||||
--tccttttttctgtatagttagtagtttctacaaatcgagtcgttgacaatgctgcttggatcggaaagtcggaataactagatgaatggctgctctgcagGTCCATCAACAACATCACGGCCCGGCGAAATCTCGGGTACCTGTCGTG-CGGGACAGGCAACCCCATCGACGACTGCTGGCGCTGCGACTCGGACTGGCAC

upper sequence: EFJ32208 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv01s0137g00240.t01 (Vitis vinifera), 3'ss of exon 1
-aacccctggtctggtctcactcttactgccgtgattcgaacgcgcgtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttctctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC------
  |    ||   |      | |   || | ||  | |  |     |    |||      |||        ||    |   | |    | || ||    |||  |||      |   ||||||| |    ||   | | |||   | | || | | |||||| || ||||||||||||||||| ||||||||| | ||| |       
gtatgaatgcgttacatatatttgaacagtcggtaattaatta-acaatgtctcaccttttt--------ttttttttttttctaaatcttgttgctgcagGAGGATCAATGCTTCAAGGAGGAAC---TTGGGGTTCCTG---TCTTGCGGAACCGGCAACCCCATCGACGACTGCTGGCGGTGCGACCCAGATTGGGAAAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttctctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC
                           gactcac  putative branch site (score: 2)
                                        ctttttttctctc  putative PPT
             tttgaaaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacccctggtctggtctcactcttactgccgtgattcgaacgcgcgtcctctttgtcctttgaaaaaaattcgactcactccgggctttttttctctcagAGGGAATGGCACACAAAGGAGGGAAGCGTTCTCGCTACTGGGCTGTGGCAGCAGCGGCAATCCGATCGACGACTGCTGGCGCTGCGACCCAAACTGGCAC

- - cctggtc
- - - - - -tggtctc
- - - - - - - - - - tcttact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcactcc