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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctgctcaactgtcaactcccaccgatcgatcacggtcacggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC

Basic information

species Zea mays
transcript AC217358.3_FGT009
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0035g01140.t01 (Vitis vinifera), 3'ss of exon 1
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgac-cggccggccatgactgcctgctct-gctcaactgtcaactcccaccgatcgatcacggtcacggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC
                         | |  |  |     |    || |    |          |  |    |  |||     |||||  | |    |   |    |   | || ||    |    ||||| || ||    ||  | || || ||||| |||||||| || ||||||||||||||| | ||||| ||||| ||||||||  | || ||    || || |
-------------------------tgttgtagatttatggttatttttatatagtattaattgttacaggtaactgtgaaagctcagatatgg--tattaattgttttttactgtatttggtt-cagGTCGAGGGACGAACTGTGAAAGCTCAGATATGGGACACAGCAGGGCAGGAGCGGTACAGAGCAATTACCAGTGCCTACTATAGGGGTGCCCTTGGAGCTC

upper sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
lower sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctg-ctcaactgtcaactcccaccgatcgatcacggtcacggacca--cagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC
                                                         |   ||| ||  ||||  |    |  |  ||||   |   |||  ||   |   || |   |  |    ||||| ||||||||||| ||||||||||| || |||||||| || || |||||||| |||||||| || || ||||| |||||||| ||||| |  || || |
---------------------------------------------------------gcaaggctat--ctgcaagagaggatttgactggtcatggccattgacaaaatgcgctgttgctctgagcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC

upper sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
lower sequence: PP1S209_94V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctgctcaactgtcaactcccaccgatcgatcacggtcacggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC
      || ||   | ||  |  | |||    | | |  |  |  |  |||  |  |||  || | ||   |   | |||| |    |||    |      | | || || ||          ||||| || || ||||||||||| || ||||| |||||||| || ||||| ||| ||||||| || ||||| || || |||||||| || || | ||| ||  
------cagcggctc-cgagtgttttatttggt-cgggggttggatgacgcacggtcgggtggacgtgg--ggagggtctgatgtgttgtgggtt------ggtggaccatgg----------cagGTCGATGGAAAGACGATCAAAGCTCAGATTTGGGACACAGCAGGGCAAGAGAGGTACCGAGCCATCACAAGTGCGTACTACCGGGGAGCCGTGGGAGCTT

upper sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
lower sequence: PP1S209_99V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------gtacggcac-cgctg-cacgcatcctctatcctctaccgccgccg--cttctcgcctgaccggccggccatgactgcctgctctgctcaactgtcaactcccaccgatcgatcacgg--tcacggacca---cagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC
                 |  | ||    ||| ||    || |       | | || | |||    | |    ||  |||  |         ||  | || | |  || ||         | |||   |   ||  |   ||||||   ||||| || || ||||||||||| || ||||| |||||||| || ||||| ||| ||||||| || ||||| || || |||||||| || || | ||| ||  
gcgagtttcggacatgttctgacatgtactgacataggtcgttgtggagccagcggctccgagtgttttatttggtcgggggttggatgacgcacggtcgggtggac-gtggggagggtctgatgtgttgtgggttggtggaccatggcagGTCGATGGAAAGACGATCAAAGCTCAGATTTGGGACACAGCAGGGCAAGAGAGGTACCGAGCCATCACAAGTGCGTACTACCGGGGAGCCGTGGGAGCTT

upper sequence: AC217358.3_FGT009 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30172 (Selaginella moellendorffii), 3'ss of exon 1
gtacggcaccgctgcacgcatcctctatcctctaccgccgccgcttctcgcctgaccggccggccatgactgcctgctctgctcaactgtcaactcccaccgatcgatcacggtcacggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC
          |   ||   |      || ||||    ||  |  |||||  || |          ||  || | | || || |    |||   || || | ||  |||         | ||   ||||||| |||||||||||||| || || |||||||||||||| ||||| ||||| |||||||| |||||||||||||||||||| ||||||| ||| ||||
----------gtaacaaaga------attctctctttccctcttttctcatctcaa---------attccttctttctatggt-ggttgtgttcttcc-cggacggatg--------gaactctagGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC

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

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: 12 (upstream exon), 38 (downstream exon)
Score: 1

CGTGGGCAAGTCCAACCTGCTATCCCGCTTCACCCGCAACGCCTTCTCCCTCGACTCCAAGTCCACCATCGGCGTCGAGTTCGCCACCCGCACCATCCAGgtacggcacc ... cggaccacagGTGGACGGCAAGACGATCAAGGCGCAGATCTGGGACACGGCGGGGCAGGAGCGGTACCGCGCAATCACCAGCGCCTACTACCGCGGCGCGGCGGGCGCGC




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