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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG

Basic information

species Selaginella moellendorffii
transcript EFJ04915
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 6
----------------------------------------gtaggaggtccttgtccttaggattgatttgtact--tactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                                         ||     |     ||  || | ||   | |||||  ||  |  ||  ||   | |  ||||||| || |||||||||||||| ||  |||||||||||||||| || |||||  ||
acttcaattatttattttaaaaccgtgatcatgcatgtacttacagactgaaattcactaagttttgatggtactaataaggtcttccttcgcactgtagGTTAACCCACATACACACCAGCTCAAAATATGTGATTTTGGCAGTGCAAAAGTTTTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv14s0066g01050.t01 (Vitis vinifera), 3'ss of exon 6
-------------gtaggaggtccttgtcc--ttaggattgatttgtacttactgcttttgtt-gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
              |    ||| |||  |   ||  |  ||| || |  | ||   |    || ||   ||||||||||||||||||  || ||||| ||||||||||||||||| || || ||||| |||
gtttgtatttgaaattcacggttcttcacgtgttctgcctgaatttttttgaccaataaaatttgttgttacagGTTAATCCCCATATTCATCAGCTCAAGCTATGTGATTTTGGGAGTGCAAAAGTTCTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv07s0005g02100.t01 (Vitis vinifera), 3'ss of exon 6
--------------------------------------------------------------------------------gtaggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                                                                                 ||    ||| ||    |    | | ||  |    ||   |||   || |  | ||||||||| || ||||| |||||||| ||||||||||||||||| || || |||||  ||
gtatgttaacgagtgaatgtattacttcatgttccactaaactgttcattttactcgtcattctttaattatttttacatttatcttgtcatttctttctctaattataagattataacacttcactttttggaacagGTTAACCCACATACCCACCAGCTAAAGCTATGTGATTTTGGAAGTGCAAAAGTTTTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtccttaggattgatttgta-cttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                                                                                                                             || || | |  |  ||| | |  |  ||||| ||   |    || ||||  | |||||| ||||||||||| || || ||||| || ||||| ||||||||||||||||| |||
gtatgtgtctcatgaatctcaatgtgtgaatgaggactcccgcagtgcatgatgttgtctattttagtactcgcattatgacgtgattactttagcaagttcctgaagcgtgtgatgttaaccagagaagttgcaagagctt-gaacggtgttgtaactgggttgagtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTTTGTGACTTTGGCAGCGCCAAAGTTCTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                                                                                                                                  |||       |   ||    | |  | |||   |     | | |     | |||||| ||||| ||||| ||||||||||| || ||||||||||| || || |||||||||
gtacgtgtgtccgacgaatcttgtcatgtgttcaagtatcttgaaaacacgatgctgactgtttaagcactcgtatttgttgctcggcatgggtggaagctggttactgagatgtttggtatgagtcacgggaaagtacaggagttgccgtggtgtcgtaacaaacttgtgtttgcatggcacagGTGAATCCTCATACGCACCAGCTGAAACTGTGTGATTTTGGAAGTGCGAAAGTGCTG

upper sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------------------------------------------------gtaggaggtccttgtccttaggattg-atttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                                                                                                                               || ||        || | |  |  |||  ||   ||    || ||||  | |||||| ||||||||||| || || ||||| || ||||| ||||||||||||||||| |||
gtacgtgtcttacgaatctcattgtgtaaatgatggcttctgaagttcgtgatattgtccgttttatcgcttgcattaggacgtgattactttagcaagtcactgaggcgtgttgtattggctacgagaagttgcaagagttggaacggtgttttaacaggcttgggtttttgtg-gcacagGTGAATCCCCATACGCATCAACTGAAACTGTGTGACTTTGGCAGCGCCAAAGTTCTG

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|169024806|gb|FE435485.1|FE435485
EST:     ACGGCGGGATTGGGGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169034065|gb|FE442799.1|FE442799
EST:     ACGGCGGGATTGGGGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169036066|gb|FE446772.1|FE446772
EST:     ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAACTATGTGATTTTGGCAGCGCCAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAA
EST: gi|169051268|gb|FE457618.1|FE457618
EST:     ACGGCGGGATTGGGGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAG
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAG
EST: gi|169066575|gb|FE474135.1|FE474135
EST:     AAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAGCGCCAAA
genomic: AAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169038251|gb|FE443937.1|FE443937
EST:     ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169033900|gb|FE441932.1|FE441932
EST:     ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169046998|gb|FE454570.1|FE454570
EST:     ACGGCGGGATTGGGGTCTGCCACCGTGATATCAAGCCACAAA-TTTATTG                         GTTA-TCCCCATACACACCAGCTGAAGCTATGTGACTTCGGCAG
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAG
EST: gi|169100546|gb|FE502721.1|FE502721
EST:     ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
EST: gi|169051816|gb|FE458998.1|FE458998
EST:     ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTG                         GTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA
genomic: ACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAA

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: 34 (upstream exon), 35 (downstream exon)
Score: 61

ATATGCCGATCTCTCGCTTACATCCACGGCGGGATTGGAGTCTGCCACCGTGATATCAAGCCACAAAATTTATTGgtaggaggtc ... gtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG
                            tacttac  putative branch site (score: 61)
                   attgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggaggtccttgtccttaggattgatttgtacttactgcttttgttgtaagtacagGTTAATCCCCATACACACCAGCTGAAGCTATGTGATTTTGGCAGCGCCAAAGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC