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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC

Basic information

species Selaginella moellendorffii
transcript EFJ06060
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os03g62600.1 (Oryza sativa), 3'ss of exon 1
--------gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttc--ttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
         || | | ||  || |   ||     |||| |  ||   | |    | |  | |  |      ||||   || |   |    ||  || | |||| || || ||||   | || || || || |||||||| ||||||||||| || ||||| |||||||| ||||| |||||||| ||||| ||||| ||  
ttaggctgttatccatgatatcacagatttttatttttatgttcagtactattgtttccccaaaggtccattgttaaattgcttcaattttgtgaccc-agGTTGAAGGAAAGATTGTAAAGGCACAGATATGGGACACAGCCGGGCAAGAACGGTACCGGGCCATCACAAGCGCATACTACCGCGGCGCAGTGGGAGCAT

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os05g01480.1 (Oryza sativa), 3'ss of exon 1
gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatgg--tggtggtgttcttcccggacgga---tggaactc----tagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
|| ||  |  | |   ||| ||  |    | | | |  |        | ||  |     ||    || ||     | | | |   |   |||     |||||||| |||||||  ||||| || || ||||||||||| || || |||||||| ||| | || ||||||||||| |||||||| || ||  | || ||  
gttactgaacactagttctctctattgaatgtaaacaaatgcattagcgttggaaaaattgaaactgatccatttgcatgaaatctttgacttgatgtagGTGGAGGGCAAGATAATCAAGGCGCAGATCTGGGACACCGCAGGTCAAGAGCGATACAGAGCTATCACCAGCGCTTACTACCGTGGAGCTCTAGGAGCAG

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AC217358.3_FGT008 (Zea mays), 3'ss of exon 1
gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
               |     | ||   | |||  ||||| |  |  ||  |   | | |         || ||| |     | ||   ||||||| |||||||||||||| || || |||||||||||||| ||||| ||||| ||||||||||||||||||||||||||||| ||||||| ||| ||||
------------gtacggcacctctgcatgctctgctcaactgtcaactcccaccgatcga--------tcacggtcac---ggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCCATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
----------gtaacaaaga------attctctctttccctcttttctcatctcaa---------attccttctttctatggtgg--tggtgttcttcccggacggatg--------gaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
          |   ||   |      || ||||    ||  |  |||||  || |          ||  || | | || || |    ||        | | ||  |||         | ||   ||||||| |||||||||||||| || || |||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| ||||||| ||| ||||
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctgctcaactgtcaactcccaccgatcgatcacggtcacggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G154960_T01 (Zea mays), 3'ss of exon 1
-----------gtaacaaagaattctctct---ttccctcttttctcatctcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
            | ||  |   |  | | |   |||      | ||| | | |  |   |  | ||    |  ||    || ||| |       ||   |   || | || || |||||  |||| || || || ||||||||||| ||||| ||| | ||||||||||||||||||||||||||| |||||||||| || ||||
ggaattccttccttactgatggtgttgtttggcttctgaagctactcgtgtta--tggatgatctcagcagaagttccttttttctcttttatttgaggc---agATAGACGGGAAGACTGTCAAGGCACAGATATGGGACACGGCAGGGCAGGAGAGGTACCGCGCCATCACCAGCGCCTACTACAGGGGCGCGGTCGGAGCGC

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
--gtaacaaagaattctctctttccctcttttctcatc--tcaaattcc---ttctttctatggtggtggtgttcttcccggacggatggaactct--agGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
                             | | | |||  || |  | |     ||  |  |   |    |   |||  |     |||   | | |  |||| || |||||||  ||||| || || |||||||||||||| || || ||||| ||||| || ||||||||||||||||| || || ||| |||| ||| 
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GLYMA02G41940.1 (Glycine max), 3'ss of exon 1
gtaacaaagaattctctctttccctcttttctcatct-caaattccttctttctatg-------gtggtggtgttcttcccggacggatggaactct------agGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
     |||  | | ||  || |    | |    || |  | |||  || |  | |         ||  |  |    | || |||   ||  |  | |      ||||||| || |||||  | || || ||||| |||||||| || ||||||||| | ||| | ||||||||||| ||||||||| | || || || || ||  
-----aaatgaatttccattgctaaatatatatatatatatattttttgtcaccagaaagaagagttataattaattccctggaaacatatatatgtttatgcagGTGGAGGGGAAGACTGTGAAGGCACAAATATGGGACACTGCAGGGCAAGAGAGGTACAGAGCCATCACCAGTGCCTACTACAGAGGAGCTGTTGGTGCCT

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggt-ggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
                         || |   ||    |   |    ||    ||||   | |      | | | |  |    || |   |||| || |||||||| ||||| || ||||| |||||||| || || || ||||||||||||||||| || ||||| |||||||| ||||| || || || |
-------------------gcaaggctatctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagc---agGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S209_99V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------------------------------------gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatg-----gtggtggtgttct------tcccggacggatggaactc--tagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
                                              |   ||  |  | |     ||   | |  ||     |   ||  |          |     |||| |  | |||      |   ||   | |||| |     |||| ||||| |||||||||||||| || || |||||||| || ||||||||| | ||||| |||||||| || || ||||||||||| || ||||| ||  
gcgagtttcggacatgttctgacatgtactgacataggtcgttgtggagccagcggctccgagtgttttatttggtcgggggttggatgacgcacggtcgggtggacgtggggagggtctgatgtgttgtgggttggtggaccatggcagGTCGATGGAAAGACGATCAAAGCTCAGATTTGGGACACAGCAGGGCAAGAGAGGTACCGAGCCATCACAAGTGCGTACTACCGGGGAGCCGTGGGAGCTT

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S209_94V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtaacaaagaattctctctttccctcttttctcatctcaaattccttctttctatggtggtggtgttct------tcccggacggatgga--actctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
  |   |   || |  | | |||   ||     |    | |    |  ||        |||| |  | |||      |   ||   | ||||  |    |||| ||||| |||||||||||||| || || |||||||| || ||||||||| | ||||| |||||||| || || ||||||||||| || ||||| ||  
cagcggctccgagtgttttatttgg-tcgggggttggatgacgcacggtcgggtggacgtggggagggtctgatgtgttgtgggttggtggaccatggcagGTCGATGGAAAGACGATCAAAGCTCAGATTTGGGACACAGCAGGGCAAGAGAGGTACCGAGCCATCACAAGTGCGTACTACCGGGGAGCCGTGGGAGCTT

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S84_180V6.1 (Physcomitrella patens), 3'ss of exon 2
--gtaacaaagaattctctctttccctcttttctcat-----ctcaaattccttctttctatggtggtggtgttcttcccggacggatgga---actctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
  |   |  | ||   |||  |     |||   | ||     ||| |   | |   || |    || |    |||||   |  | | || |    |  ||||| ||||| |||||||||||||| |||||||||||||| || || |||||||| ||| | || ||||| || || ||||| || ||||| || || ||  
cagctgcttaaaacattctggtgatgacttaggtgatgcactctccagcacttggcttttg-aatgctctaattcttggtgttccgctgcattaccattagGTTGATGGAAAGACGATCAAAGCTCAAATCTGGGACACAGCAGGACAAGAGCGATACAGAGCTATCACTAGTGCGTACTATCGTGGCGCTGTAGGAGCTT

upper sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S21_298V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaacaaag---aattctctctttccctcttttctcatctcaaattc---cttctttctatggtggtggtgttcttcccggacggatggaactcta---gGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
 | ||| |      |  |||  |    ||||   | |     |  |     ||  || | |||  ||  |    ||    | |       | | ||   ||| || || ||||| |||||||| ||||||||||| ||||| || || ||| | ||||| || ||||| || || |||||||| ||||| ||||| || |
ttgacagattttggtcatctagtgatgtcttagatgacgcgtagctaagaatttgttgtctggaagttctaacttttagtgtccttctttattttattagGTCGACGGAAAGACCATCAAAGCTCAAATCTGGGATACGGCAGGTCAGGAGAGATACCGAGCTATCACTAGTGCATACTACCGTGGCGCTGTGGGAGCTC

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), 34 (downstream exon)
Score: 7

CGTCGGGAAATCCAACTTGCTCTCCAGATTCACGCGCAACGAGTTCTGCCTCGAGTCCAAATCCACAATCGGGGTCGAATTCGCGACGCGCACGATCCAGgtaacaaaga ... ggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaattccttctttctatggtggtggtgttcttcccggacggatggaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
            tttctat  TA-rich tract