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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactcctcgtcacacactttgttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG

Basic information

species Selaginella moellendorffii
transcript EFJ23417
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 2
----------------------------------------------------------gtatgatcgagagc--tacaccttttcttcctctcctttctcgtgtgtgtattaactcct-cgtcacacactttgttcctca----agGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                                                           ||  |||  | ||  |      | |||     |      |||||  |      || | |    | ||  | ||  ||  ||    |||||||||||||||| |  ||| |  | ||||| || || |||||||||||||| |||||||||||||||   || | | | |||||||||||||||||| 
gtgagtgcgtgccagtatgccattagttcagtagttcttcatttttttttaaaaaaaactacaatctggtgcagtcggttgtgtctaaggatttaaattcgtggattgggagacacgtgtagctcatccgttcctctgcatttcagGTGCCAATTGGCGGCGCGTACAGGCTCATCGACGTGCCGATGAGCAACTGCATAAACAGCGGGATCAACAAGGTCTACATCCTCACGCAGTTCAACTCGC

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv05s0020g02880.t01 (Vitis vinifera), 3'ss of exon 2
----gtatgatcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactcctcgtc-acacactttgt-tcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
    ||    |   ||   | |  |        | |  ||   |   |    ||    |  |  |  | | | |  || |  |  |||| || ||||| ||    ||  |  |||| ||||| ||||||||||||||||||||||| || ||||||   || | | | ||||| || ||||| || |
gtaagtccactttggaagca-atgtggggcatttttttttatacagattccaataggtttataatttagaaaatgggtgtattgtagGTCCCGATTGGAGGGTCATATAGGCTGATTGATGTGCCAATGAGCAACTGCATCAACAGTGGAATCAACAAGGTCTACATTCTCACTCAATTCAATTCAG

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S2_204V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------------------gtatg-atcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactc-------------ctcgtcacac--actttgt---tcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                                                                                                 | | || ||  | || | | |   |     |   ||  |  ||||| || ||| |             ||||| ||    | |||||   |  |  ||||||||||||| ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| ||||||  ||||||| | ||||| || ||||||||  
gtaagccccttaacacatcctagaatttgtgtttgcaaactcttctctgaagctttgtcttcttcaatttgttgatgcttgtttgaaaacaaactagacgcatagaatgttaaaacctcattataattttattgaca-gtgtgaatgaaccctggttagtgaaaactcgtgactgtaattttgtatgtattgcagGTGCCAATTGGAGGTGGCTACCGGTTAATTGATGTGCCCATGAGTAACTGTATCAATAGCGGAATCAACAAAGTTTTCATCCTCACCCAATTCAACTCCA

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S98_52V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------gtatgatcgaga--gctacaccttttcttcctctcctttctcgtgtgtgtattaactcctc-gtcacacact--ttgttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                | |||  |     | ||    | || |       |||          |  ||   | ||| | ||| | |   ||| |   || ||| ||| |||| |||||||| || ||||||||||| || |||||||||||||| ||||||||||| |||    |||  || ||||| |||||||| ||  
ctatctttttttcttttctgacaggtgttggtaggtttattgtcgaaaaacttatgtacaaccgggttggtttctctgacactcgccaattggtgaaca-gGTTCCACTTGGGGGTGGCTATCGATTGATCGATGTGCCCATGAGCAACTGCATTAACAGCGGGATTAACAAGATTTATGTTCTCACTCAGTTCAATTCTA

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S36_158V6.2 (Physcomitrella patens), 3'ss of exon 3
---------------gtatgatcgagagctacaccttttcttcctctcct---ttctcgtgtgtgtattaactcctcgtcacacactttgttcctca-agGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                 |    ||| || |     ||   ||  | ||     ||||  ||     ||  |  |   |  ||      || |    | |||| ||| |||| |||||||| || ||||| |||||||| |||||||| || |||||||| || ||||||    ||| ||| |||||||||||||| ||  
gatcagcaatcacgctgaactccgacagatctgggttggtttgttgtcgacgattctactggcaagatcgatcctctgatactggtcatggtttgaacagGTTCCACTTGGAGGTGGCTATCGGTTGATTGATGTTCCCATGAGCAATTGTATCAACAGTGGAATCAACAAGATTTACGTTCTCACGCAGTTCAATTCTA

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S237_47V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------gtatga-tcgagagctacacc-----ttttcttcctctcctttctcgtgtgtgtattaactcctcgtcacacactttgttcctca--agGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
           ||  || | |||| ||  |         || |||      | |||    || |    ||||  ||     |   | | |   | |  |||||||  | ||||| | ||||||  |||| ||||| || ||||||||||||||||||||||| ||||||    | | ||| || ||||||||||| ||  
aacaccttttggtgcgaattgagatctgtagtagagggcttgttcacaatttctctgtgatgggacccaactgatcaattgagtttgtatctgtaattagGTGCCGCTCGGCGGCGCCTACCGACTGATTGATGTGCCGATGAGCAACTGCATCAACAGCGGAATCAACAAGATCTACGTTCTTACGCAGTTCAATTCCA

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S397_21V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------------gtatg-atcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactcctcgtcacacactttgttcctca--agGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                                                                                                 ||  | ||    ||||      || |      |      | |   |  ||  | ||  || ||      | |||   | |  |||||||  |||| ||||  ||||| ||||| || || || ||||||||||||||||||||||| ||||||    |||  || ||||| || ||||| ||  
gtaaggaccactttcttcttacaggccattctagctaatcgtacacaatgaaagtctaaataatgccgttgtagaagtgtactgtctcctggttggcgtgggtatttgtagctgggggattgcacatgattggaagttgaagggatag-agctaatcttctgtatttgtgtatgtgatcagGTGCCTCTTGGAGGTGCGTACCGATTGATTGACGTGCCGATGAGCAACTGCATCAACAGCGGAATCAACAAGATTTATGTTCTCACTCAATTCAATTCTA

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------------------------------------------------------------------gtatgatcgagagctacaccttttcttcctctcctttctcgtgtgtgtattaactcctcg----tcacacactttgttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                                                                                                                    ||  ||| |  |    || |  |  | ||| |  | || |||||  |   |  |    |      |  |   |   |  |  ||||||| || || ||||  ||||| ||||||||||| || |||||||| ||||||||||| || || |||  ||| ||  | || || || ||||| ||  
gtaagcttctccctcattcaagagtctgtgttggcagtgcactattctaagcccctacgattaataatatgtttgttgttatcagaatcaaaacgaatgaaatcctgtgttaattataccatcaaacgtgcaacataattgttctc-cagtactggtgtgaatgccagttgggtgagtcctatgcgtctctgtattgcagGTGCCTATCGGAGGTGCGTACCGATTGATCGATGTACCCATGAGCAATTGCATCAACAGTGGCATTAACAAAGTCTTTATCCTTACTCAATTCAATTCCA

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|169065580|gb|FE474833.1|FE474833
EST:     GCGTTGGAACGCGATTGTTTCCCCTCACAAAGCAAAGGGCAAAGCCTGCG                         GTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGC
genomic: GCGTTGGAACGCGATTGTTTCCCCTCACAAAGCAAAGGGCAAAGCCTGCGgtatgatcga ... gttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGC
EST: gi|169040801|gb|FE447852.1|FE447852
EST:     GCGTTGGAACGCGATTGTTTCCCCTCACAAAGCAAAGGGCAAAGCCTGCG                         GTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGC
genomic: GCGTTGGAACGCGATTGTTTCCCCTCACAAAGCAAAGGGCAAAGCCTGCGgtatgatcga ... gttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGC

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: 22

GACCCCGCGCGTGGATCCCAAGTCGGTCGTCTCCATCATCCTGGGAGGCGGCGTTGGAACGCGATTGTTTCCCCTCACAAAGCAAAGGGCAAAGCCTGCGgtatgatcga ... gttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctcctttctcgtgtgtgtattaactcctcgtcacacactttgttcctcaagGTGCCAATTGGCGGTGGCTACCGCTTGATCGATGTTCCAATGAGCAACTGCATCAACAGCGGGATCAACCGAGTTTTCGTACTCACGCAGTTCAACTCGG
                     tattaac  putative branch site (score: 22)
                                         ctttgttcctc  putative PPT
                   tgtattaa  TA-rich tract