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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattcatggcgttgtttataggtttcctacttttgtaggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT

Basic information

species Zea mays
transcript GRMZM2G141241_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g43140.1 (Oryza sativa), 3'ss of exon 4
-----ttattcatggcgttgtttataggtttcctacttttgtaggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
     |  || |     ||   |    || | | | |||  || | |  ||  |   ||    | |   ||    | ||||  ||| |||  |||    ||||||| || || ||||||||||||||||| ||||| || |||||||||||| |||||| 
agaaatattttaaaaaatttcatgactgtatgc-attttcatatgtaaggattaaaaattggtcgtaggtt----ccctcattaatagtcgtgttctgattgcagGGCCAGACGACATGCCAGCACATATTAAATCGTCGATGTTTGGTTGTGCCCTGAC

upper sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G17340.2 (Glycine max), 3'ss of exon 2
ttattcatggcgttgtttataggtttcctacttttgtaggcagagaccatgtatc--atgcatgattt---agatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
      |  | ||||  |      ||| | |     | | ||   | | || ||   ||  ||||  |   || ||| | |     |    |  |  | || |||| || ||||||||||| |||||||| ||||| || |||||||||||| | || ||
----caactgtgttggcttgtacattcttgcaaaaat-gtcaactatcttggatttgattgatgacatgccagctcatttaatttctacatatgtataatttcagGGCCAGATGACATGCCGGCACATATTAAATCGTCGATGTTTGGTTGTGCACTCAT

upper sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G34680.2 (Glycine max), 3'ss of exon 4
-ttattcatggcgttgtttat-aggtttcctacttttgt-aggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttca--tttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
 | | ||| |  |||  |||| | || |  | ||  ||| |||| |  |   | |  |||  || || || ||   |  |  ||| |  | ||  |  |||||||| || |||||||||||||| ||||| |||||||| |||||||||||| | || | 
ataagtca-gttgttacttattaagtgtaatgctgctgttaggctgtta--gttttccat-tataatatacatatttttctgatt-tggatttgaaattttgcagGGCCAGATGACATGCCAGCTCATATTAAATCATCGATGTTTGGTTGTACACTCAC

upper sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT1G21065.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------------------------------------------------ttattcatggcgttgtttataggtttcctacttttgtaggcag-agaccatgtatcatgcatgatttag--atcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
                                                               | ||  |  | || |     |   |   | | |  | ||||  | | |   | ||||| ||  | | |  || |      ||||||      | ||| ||||| ||||||||||||||||| |||||||| |||||||||||||| |||   || | 
gttagttgttggtttcatcagactaaagctaatttatatatgaacacacgataaaatcaaagatgttgttccctttatcctctgaaatgtgattctctttggcattacatctgatttcatgaattttgttgtaattagatttgaattgtgttaaataatt-gcagGTCCTGATGACATGCCAGCTCATATCAAGTCATCAATGTTTGGATGTCAACTCAC

upper sequence: GRMZM2G141241_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0122g00190.t01 (Vitis vinifera), 3'ss of exon 4
--ttattcatggcgttgtttataggtttcctacttttgtaggcagagaccatgtatcatgcatgatttagatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
    |   ||    |   | |||        |      || | ||| |   |  || |    |     | |  | | |    |   |  |   | ||| |||| || ||||||||||||||||| |||||||| ||||||||||||||    || | 
tgacaaatattagataaatgataaaaaaggaaagcaaataag-agaaattgttcataagaagtttgccacaaaattgattc-taaccctgcaaccttttcagGTCCGGATGACATGCCAGCACACATCAAATCTTCAATGTTTGGTTGCAGTCTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accatgtatcatgcatgatttagatcactcacaaattgtcaagtttcatttgcagGACCTGATGACATGCCAGCACATATCAAATCATCAATGTTTGGTTGTTCCCTGAT
                         cactcac  putative branch site (score: 2)
                                           tttcattt  putative PPT
              atgattta  TA-rich tract