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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

Basic information

species Zea mays
transcript GRMZM5G824405_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 5
-------agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
       ||   |||  ||| | || |||   |||| ||   ||  | |  |||        || ||    |||||||||| | | |    | |||||  ||||||||||||| | |||||||| ||||||||||||||||| ||||| |||||||| || || ||||||||||||||||||||||||||||||||||||||||||
catatgaagaatgaataatttctgtcaatgtgttgaaatactttattatgcttca-------aattacctttgcagttcttctgtaaccattgtgctgccattctagGTTGGGTTGCCAGCTCGTGGTAAGACCTTTACAGCGGCTAAGCTTACAAGGTACCTTCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
--agctggaac--tattccagtt---aatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   ||   ||    ||| |  ||   | | |||  |  |   |   |||  || ||| |   |||||    |    ||  ||||||| | || |  | || |   |||| || || |||||  ||||||| || || || ||||||||||||||||||||||| || |||||||||||| | || ||||||||||||||||| |||
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttggttttttaa---aagtaaat-tatttttaattttttactaatttttttatgt---agGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    |||||  | |    |   |||||    |  || |      |       |  |   ||   |   | ||   |||||||  |  | ||  |||  ||||| || || ||||| |||||||| || || || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatg-tagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttt-tttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 | ||||||  |     |  |        |  |||  ||| |    | |   | |  |  ||   || |  |   |  ||| || |  | ||  |    |||||  |  | ||||||||||| ||||| |  || ||||||||||| ||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaaatgccacattccc-atctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttctt-ttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 6
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 | ||||||  |         || |  |    |   |    || |||  |  |   || |||       |     ||| |||  |  | ||  | |  |||||  |  | ||||||||||| ||||| |  || ||||||||||||||||||||||| ||||||||||||||| | || ||||||||||||||||| |||
tacctggaaaaaaaatgccacattcccttctgtacttcatcttatttagtaaaataaaatatttgaaatgaataatttctaactagtttctt-tttcttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
--agctggaac--tattccagtt---aatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
   ||   ||    ||| |  ||   | | |||  |  |   |   ||| ||| ||| |   |||||    |    ||  ||||||| | || |  | || |   |||| || || |||||  ||||||| || || || ||||||||||||||||||||||| |  |||||||||||| | || ||||||||||||||||| |||
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaa---aagtaaat-tatttttaattttttactaatttttttatgt---agGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------------------------------------agctgga-actattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgca------gttctttttttaatcat--ctgctgatatt---ctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
                                                                            |||||||   | ||   | |      || |  |  |||     | |   |  | | ||  |   |   |      |||||  ||   | |||  | |   | |||    ||||||||  | || |||||||| ||||| ||||| ||||| ||  | ||||||||||| || ||||| || ||||| || ||||| || ||||||||||||
gtatttgtagccacatagatgttggtcatagtttctgcaggtcttttagcttatgtttcctagtttgattgtaaggagctggacgttgttgtggctggctattttatttaacttataaacgtaaatggaaaaaaaaaaaaaaagactggatgttctgattcacaccattcccgtcaaaattgtattagGTTGGCTTGCCTGCTCGAGGAAAGACTTTTACTGCAGCAAAGTTGACAAGATATCTACGCTGGTTGGGACATGATACTAAACATTTTAATGTTGGAAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctg----------atattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
    | ||||  |||||| |   ||    | |   |   ||| || |    | | |   ||  |  || || | ||   ||| |   | ||          |||||  |||||||  | |||||||||||||| || ||||| ||||||||||||||||||||||| || ||||| |||||||| || |||||||||||||||||||||
----gcaact--tccagtaa---cagcaggttaattccatttgttgcacctaaaaattcatttac-caattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S235_92V6.1 (Physcomitrella patens), 3'ss of exon 5
-agctggaactattccagttaatccattgagat-gtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatat-tctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 |    |||||  |    |||     || || | | ||   |     | |   || |   | | || |||  |    |  | | | | |  || |   |  ||||||| ||||| |||||||| ||||| |||||||||||||| || || ||||||||| | ||| | || ||||| || |||||||||||||||||||||
tacaacgaacttcttacattacaagcttaagttcgactgcttgaaaatatcatagct---tcttcaagcatgttacatactgaacttgtcatggtggattcagGTTGGCCTACCTGCTCGAGGGAAGACTTTTACAGCAGCTAAGCTGACGAGATATCTCAGGTGGCTTGGCCATGATACCAAACACTTCAATGTTGGAAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S215_89V6.1 (Physcomitrella patens), 3'ss of exon 7
-----agctggaactattccagttaatccattgagatgtctttctttctttctttcagataag-tatgcatgcagttctttttttaatcatctgctgata-ttctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
       || | | | |     | |    ||   |   |  |       |||   | | |||| || ||  | ||||        ||| |    |||||  ||  |||||||| |||| ||||| || ||||| || || ||||||||||| || |||||| | || |||||||||||||| || || |||||||||||||| |||
tgctttcctagtagtgtattgttgagcgtataatgtgattgtggccaaattcacgctgttaagctacgctgggagttg-------aatgagtctctgatggtttcagGTTGGGTTACCGGCTCGTGGAAAGACATTCACTGCAGCTAAACTGACCAGATATTTGCGGTGGTTAGGTCATGACACCAAGCACTTCAATGTTGGCAAG

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 6
-agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgc--agttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
 ||| |  | ||  | | || |  ||  ||   |||  | |||| |      | ||  | ||   |    | |   |  |   |     ||||     |  |||||||| |||| || ||||| ||||| ||||| ||||| ||| | || ||||||||  | ||| |||| ||||| || |||||||||||||||||||| 
cagc-gcgattaaacgaattgaagca--gaagcgtcgatttttcatgtgaaaatattggaatttctttcaaataactcatcctactggttgctttgggttcagGTTGGGTTACCTGCACGAGGCAAGACGTTTACGGCAGCAAAATTGACGAGATATCTTAGGTGGCTAGGCCATGATACTAAACACTTCAATGTTGGAAAA

upper sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattcta--gGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
                                                      ||  | ||    || |  |   | | ||| |    |    |||||  ||| ||  |||||||  | || || || || || || |  || || ||||||||||| || ||| | |||||||| || ||||||||||| |||||||| 
-----------------------------------------------------gtagat-tgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcagataagtatgcatgcagttctttttttaatcatctgctgatattctagGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG
                                         tgctgat  putative branch site (score: 3)
                        ttctttttttaatcat  TA-rich tract