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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggcgactgaactgtttcttttttttgtttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG

Basic information

species Selaginella moellendorffii
transcript EFJ11344
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G006714_T01 (Zea mays), 3'ss of exon 4
-------------gtaagttggcgactgaactgtttctttt-----ttttgtttggttttgacatgctgct--------------taccgatgtta---cgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
              |   |   |   ||   | ||| | ||      |||||  | |   || |  | | |              |||  || ||    | ||  ||| ||| ||||||||||||||||  |||||||||||||| | ||||| |||||||||||||| |||||||| || ||||| |  |||||||||  ||||    |   |||
gtaattgaatataattgctctacacttggtttttttttgttcaattctttgtccgttcacgagacacggatagcgtagcgtctgatacaaattttggttcctgaactcgtgt-cagTGTACAAGAAGCACCATCCACCTGCATTAGCCGACGACGTGTGGCGTCTGGAGAAGATCGGGAAAGACGGCGTGTTCCACAAGAAGCTGGCGGACTTCGG

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GRMZM2G427418_T01 (Zea mays), 3'ss of exon 4
--gtaagttggcgactgaactgtttctttttt-----ttgtttgg---ttttgacatgctgcttaccgatgttacgtgcgctcttgtg----cagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
   ||| ||   |    |    |||| ||        ||| |||    ||||   |  ||   |||  |||  || | ||  ||  |     ||||||||||||||||  |||||||||||||| | ||||| |||||||| ||||| |||||||| || ||||| |  |||||||||  ||||  | |   |||
gtataaatttctgtgccattattttccttgccacgaattgcttgtgtttttttgaactctagatacttatgaaacttccgtcctgataaatccagTGTACAAGAAGCACCATCCACCTGCATTAGCCGACGACGTGTGGCGCCTGGAGAAGATCGGGAAAGACGGCGTGTTCCACAAGAAGCTGGCTGACTTCGG

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
--gtaagttggcgactgaactgtttcttttttttgt-----ttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
   |    |    |     |  |||||| |   |||      |||| || || |  |       ||||     | |  |  ||||||||||||||||||||||||||||||||  | |  || || |||||| |  |||| |||||||| ||||| ||||| ||||| ||   ||| | |    | ||
gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagttggcgactgaactgtt-tcttttttttgtttggttttgacatgctgcttaccgatgttacgtgc---------gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG-
||| ||       |    |||| |||||||    | || ||   || || |   | |  |    || ||          | |  |||| ||||||||||||||||||||||||||| || |  || ||||||||| |  | || ||||| || || || ||||| || || ||| |||| || |    | | 
gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttcttctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCT-AACCGCTGCAGG

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------gtaagttggcgactgaactgtttcttttttttgtttggttttgacatgctgcttaccgatgttacgtgcgc-tcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
                                                                                 || |  |   |   ||    ||    | ||| | | | |  ||  |  ||   | |  |  ||| || |  | | ||||||||||||||||||| ||||||||||| || |  |||||||| |||||  |||| ||||| || |||||||| || || |||||||| || |||||||||  
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatttatctagatg-gaagtattga--atcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S98_167V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------gtaagttggcgactgaa--ctgtttcttttttttgtttggttttgacatgctgcttaccgat-gttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
                 |  |||     |||||  | ||   |       |     |  |  |    |   ||   || |||    |    ||||| |||| ||||||||||| ||||| ||||| ||||  |||||||| |||||  |||| ||||| ||||| ||||| ||||||||||| || || ||||||    |
tgccctgtgcacatccattcgttctgtgctgaatgccgtgattaacagaagaaaaatcatatctctatatctaataattgttgttggtcaccttgtacagTCTACAAGAAGCACTATCCGCCTGCTTTAAATGACGAGGTTTGGCGATTGGACAAGATTGGAAAAGACGGTGCTTTCCACAAACGTCTAAATCAAGCAAG

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S51_322V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------gtaagttggcgactgaactgttt---cttttttttgtttggttttgacatgctgcttaccgatgt-tacgtgc----gctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
             |||||   ||   ||    |    |    |  |  ||| ||        |  ||||| | | | |  ||||     || | ||||||||||||| ||||| || |||||||| || |  ||||||||||||||  |||| ||||| || || || || |||||||||||||| || ||||||  |  
ttgttcggtgccaaagtttttgaaaaaaagaatcaggcagcatggtacttgattggatgcaaccacttacagttttctttgtgctgaaactttcgtgcagTGTACAAAAAGCACTACCCACCTGCCTTGAATGACGAGGTGTGGCGCTTGGACAAGATTGGGAAAGATGGTGCTTTCCACAAGCGTCTTAATCAAGCCAA

upper sequence: EFJ11344 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S34_132V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------gtaagttggcgactgaactgtttcttttttttgtttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
                   || |   |  ||   ||       |  |    |       |     |  |  | |    ||||           ||| |||| ||||||||||| |||||||| || || |  |||||||| |||||  |||| ||||| || || ||||| |||||||||||||| || ||||||     
tctgccagatttccaagttgtgatcagaagaagaaagaagggatggtgaaagcccaacatatctgtatttttgattattgttgttgattactctgttcagTTTACAAGAAGCACTATCCACCAGCCTTGAATGACGAGGTTTGGCGATTGGACAAGATTGGGAAAGACGGTGCTTTCCACAAGCGTCTAAATCAAGCTCA

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: 80

TTCAGGCTTGGGGTCCGGATGTCGGGAGCTAGCAGCGAAGTTCTTCGTATTCGAGAAGCAAAGACAGAATCGTTCACAGTGAAAGATCACAGAGGGGAACgtaagttggc ... tcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgtttggttttgacatgctgcttaccgatgttacgtgcgctcttgtgcagTGTACAAGAAGCATTATCCACCTGCATTAACGGACGAGGTGTGGCGTCTGGATAAGATCGGAAAGGACGGGGCTTTCCACAAGCGGCTGAATCAAAACGG
                       tgcttac  putative branch site (score: 80)
                                          cgctctt  putative PPT