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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

Basic information

species Selaginella moellendorffii
transcript EFJ16306
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os03g58530.2 (Oryza sativa), 3'ss of exon 3
gtctcgttgtgttcga-acttctctttcctctcttggtctcgt-tgtgatcgaa-cttctctttcttctcttgtgttcttaccaagcgctttatt-acgtga-agGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
     |      | || |   ||||    | |  | || |      || || |  ||||  || |     |  | |  ||     |   || ||| || | | |||| ||||||||||||||||||||||||||| ||  |  | ||| | || || |||   |||   || ||
-----gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatctgttgttgattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 3'ss of exon 2
--------------------------------gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgat-cgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
                                  | |  ||   |      | | ||   | ||   |    |||   ||    | | ||  ||| |||||  |  | ||  |     | || ||   ||||| || ||||| ||||||||||||||||| ||||| ||| | ||||| ||||||||   ||||||||| ||
gtatgcttgaatgctgattgttcatttcccgttccccagtgcaatgttggatttgttcaatttccatgggatgttagaatgttgattgctgattcgtctctgcttgtgttttctttttcgtttttc--tgaagATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G119357_T01 (Zea mays), 3'ss of exon 2
gtctcgttgtgttcgaacttctctttcctctcttggtctcgt-tgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
||   |   |  || | | | || ||  |  |||  |||  | ||||   |   ||          | |  |  | |      | |  || ||   | |||||||||||||||||||||||||||||| ||||| ||  | ||||| ||||||||  | |||||||| ||
gtacggagctcctcaatcctttcattgttgactttttcttctctgtgcatgcgttttgagcctgcttgtgataatttgggtgtgtgtatttttctctaaagGTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G871463_T02 (Zea mays), 3'ss of exon 2
gtctcgttgtgttcgaacttctctttcct--ctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
|| |     |  || | | |  | || ||  || |   | |   ||||   | | || |   |    | |  || |            ||| |  |   |||||||||||||||||||||||| ||||| || || ||  | ||||| ||||||||  | |||||| | ||
gtatgaagctcctcaacccttccattgctggctgtcccttttactgtgcatgcatttttagcttgcttgtgatgattgggttgtctattttctctc---aagGTATTGCAAATGTGAGATGCCGTACAACCCCGATGACCTCATGGTGCAGTGCGATGCTTGCAAGCACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA06G34850.1 (Glycine max), 3'ss of exon 1
gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcg------ctttatta--------cgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
              | |    | |||    | |  | | ||  | | |     || | ||| || |   | |          |||      |||| ||           |||||||||||||||||||||||||| || || ||||| ||| | ||||| || || ||    |||||||||||
--------------ggaggggtttttttggtttcaggcccgagggggttccttttttttttttttttggggggggggggggggcgggggggcttttttggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA12G20180.1 (Glycine max), 3'ss of exon 2
-gtctcgttg--tgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
    |  |||  |||  | |      |||    | ||||    | || |      ||| | |||||| |||||   | ||     | | ||| |    |||||||||||||||||||||||||| || || ||||| ||| | ||||| || || ||    |||||||||||
gaggttattgattgtggggatggggattttgggttttggaactgatggggcttttctttt-tttcttttcttgaacttttttt--gtggtttgtgttttgaagGTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT4G22140.1 (Arabidopsis thaliana), 3'ss of exon 2
gtctcgttgtgttcgaacttctctt-tcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
   |   |   |    | |  ||   ||    ||  | ||  || | | |     | ||  |  | | || |  | ||       | | |      |||||||| ||||||||||| ||||| |||||||| |||||| | ||||| ||||| ||   |||||| || ||
--gtaagtagataaatagtaatcagatcagaactacgccttcttattacctggaatttccatgattttttat-ctgttgtgggttgttgttggttctgaagGTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S56_182V6.1 (Physcomitrella patens), 3'ss of exon 2
gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaac--ttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
      |||  || | | ||   | | |      | |  | |    |   |||  | ||  | |     | ||  || |  |   |   |  |    || || |||||||| ||||| |||||||||||||| ||||| ||||||||||| || ||   |||||| || ||
-cgattttggctttgtagttacatcttcctgaaagatgccttaaatagaaaacaatccttgtgccgtattagtaatcgtgaccttcaactggt-gtatgcagTTATTGCAAGTGTGAAATGCCATACAATCCTGACGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
--------gtct--cgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
        |||    ||         | ||   |    | | ||  | || |||||||  ||   ||    | | |  |||  ||| ||         | ||  ||  |||||||| |||||||||||||| || ||||| || |||||||||||||| || ||| | ||||| |||||
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttc-ttgtgatataaaggctgacccatttggtgttctctgac---------tgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG

upper sequence: EFJ16306 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S384_37V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------gtctcgtt--gtgttcgaacttctctttcctctcttggtctc--gttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtga---agGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
                                                                             |  |||  | ||| |  ||||| |    |    ||       |||  | | |  |   |      | | | |  ||| |    | |     ||   |||    ||||||||||| ||||||||||||||||| || ||| |  ||||| |  | ||| |    ||||| || ||
gtaaggctccgcattgcatgaatgagtcgtttaagatgggcataacctatgaagtttgcgtgtggtaatgcgcagcgcatgttaggcgttgggtcttctgtgaggtgcagtgagtcagggttaggtttgtgcagttaacgactttgtcgatttcgttgataacttggaatggggtgtttcagGTATTGCAAGTGTGAGATGCCATACAACCCTGACCACGTGATGCTGGAATGCAACAGTTGCAAAGACTG

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: 13 (upstream exon), 23 (downstream exon)
Score: 1

AGAGCTACACCAAGTTGGAGAGCGTGGGAAGCGATGATTTCTTCTACCGATTCGAGTACAAGGCGGCCACAGGCGGCTTTACTCCCGATCGTGTTCCAGTgtaagtgctc ... ttacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG
                           ttcttac  putative branch site (score: 1)
                                        ctttatt  putative PPT
                                         tttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcgttgtgttcgaacttctctttcctctcttggtctcgttgtgatcgaacttctctttcttctcttgtgttcttaccaagcgctttattacgtgaagGTATTGCAAATGTGAGATGCCATACAATCCGGACGATTTGATGGTTCAGTGCGAGTCCTGCAAGGATTG

-tctcgtt
- - - - - - - - - ttctctt
- - - - - - - - - - - - -tcctctc
- - - - - - - - - - - - - - - - -tggtctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcgct