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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC

Basic information

species Zea mays
transcript GRMZM2G147145_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g49810.1 (Oryza sativa), 3'ss of exon 7
gttagtttaatgcatc-ttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaat-tatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
|| |||  |||  |   |||||  ||||| |   || ||||            || ||||||   ||  | ||||        | |  || |  |   |   ||||||||||||| ||||||||||| ||||||||||||||||| ||||||||||| || |||||||||||||||||| ||||||||||||| ||||| |||||||
gtaagtgcaatctagagttcaatttggaattgcaatttcttgg----------caatgactgagaaacatgtattcggtaaaaactgctcatttttctaccatgcagGAGCCTGAGAAACATGTATTCCATCTTGTTACTGACAAGCTGAACTTTGGAGCAATGAACATGTGGTTTTTGTTGAATCCACCTGGAGATGCGACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G40260.1 (Glycine max), 3'ss of exon 8
--------------------------------------------------------------------------gttagtttaa---tgcatctt-caagctggaaatatgatctcttcattgtttgtacc--attgactggtcaattatattacact-------------cttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                            || |||     ||||   | ||| | ||| ||||  | | |     ||   | ||  | | | |    |||   |||| |||             ||||| ||| |  ||  ||  |||||||| |||   || ||||| ||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||| 
gtgacttaaacagtcttttaccataccagtgtgtatgtgcatgtctatatagatattcttttatatagatgatgaataatttgtgcttgcactgtacaacccggacatattttgtttgtgcagtgcatccctgactcagtaaataatataattaaactttgccttcattatcttatgtttgtgtcttcaacattgcagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA07G08910.1 (Glycine max), 3'ss of exon 5
-----gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
        | | |  ||||| |  ||| || |  ||||||   ||  |   || |||  || |     ||      | | |   || || || |  ||  ||  |||||||| |||  ||| ||||| ||||| |||||||| || ||||| || ||||| |||||||||||||||||| |  | || || ||||   | || |||||||
gcaccaaaaatatcgtgcatgtgaaag-tgtatctatgat---ttagtaaattatacttttaa--aaccag--gcctcataactttgttattgt--cttcaacgttgcagGATCCTTCAAAGCATGTTTTTCACCTTGTTACCGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTCTTTTAAACCCTCCTGAAAAAGCTACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G45750.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------gttagtttaa---tgcatctt-caagctggaaata---tgatctctt---cattgtttgtaccattgactggtcaattatattacactcttatttttct---------tgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                             || |||     ||||   | ||| | ||| |||   || |  |||   |||   |   |  ||  |      ||||| | |   |  | ||| |  |         |  |  ||  ||| |||| |||   || ||||| ||||| ||||||||||| ||||| || ||||| ||||||||||||||||||||| ||||||| |||||  | || |||||| 
gtgacttggactgtctttttccataccagtgtgtgtgtacatgtctgtatagtgaatttttttttatagatgatgaataatttgtgcttgcactgtacaacccggacatagtttgtttgcttgtgcatccctgacaaaataaataatataattaaactttgccttcattatcttatgttcgtgtcttccaacgttgtagGATCCTTCGAAGCATGTGTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAACATGTGGTTTTTGTTGAATCCTCCTGGAAAAGCTACAATCA

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA03G02250.1 (Glycine max), 3'ss of exon 13
--------------------------------------------------------------------------------------gtta-gtttaatgcatcttcaagctggaaatatg---atctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                                         | | | ||   ||| |  |  || || | |    ||   ||  |   || ||  ||| |      ||  |     ||    |   |||||  ||  ||  |||||||| ||    ||  |||| ||||| ||||||||||| ||||| || ||||| ||||||| |||||||||| |  | || || |||||  | || |||||||
gtgacttgggctgtctttttaaccataccagtatttgtgtgcaagttcattgtttccttttatagattgcaaataagggtgccttgaccatggtcaacatatcgtgcatgtgaaagtgtatctatgatttagtaaattatattattaa------aaccaggcctcataacttagtttctgtcttcaatgttgcagGATCCATCGAAGAATGTTTTTCACCTTGTTACTGATAAACTAAATTTTGGAGCCATGAGCATGTGGTTTCTTTTAAACCCTCCTGGAAAAGCTACAATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0048g01300.t01 (Vitis vinifera), 3'ss of exon 8
gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
     ||  ||          |       || ||   |   |  |    |  |||    |  ||  || |  | ||||    ||  |  | |  |  ||| |||||| || |||||||||||||| ||||| |||||||| || ||||| ||||| |||||||| ||||||||| || |||| || || ||  | ||||| ||||
----tttggataagcgaaaggggatttgttaggaaagcacaaaagggcatcacatatgttcttcctttttcattcactaagtttgctaataccctcgatt-gcagGAACCAGAAAAACATGTATTCCATCTGGTTACTGATAAGCTGAATTTTGGAGCCATGAATATGTGGTTTCTGTTGAACCCCCCAGGAAAAGCAACTATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S251_8V6.1 (Physcomitrella patens), 3'ss of exon 8
gttagtttaatgcatcttcaagctggaaatatgatctcttcattgtttgtaccattgactggtcaattatattaca---ctcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
     | | |   | | |    ||       |  |   || |  | ||  |  ||   ||  ||  |||| || ||   |     | ||   |||| |     ||||||| ||    || ||||| |||||| ||||||| ||||||||||||| ||||||||||  ||||||||| ||||| || || || || | ||| || ||||
---gctcttacatagcataggtctattttctttttagttttagcggtttgagaataagcttctctgttattttgcaaggcctaagtgttatctgctgt-----tgcagGATCCCAGTAAGCATGTCTTTCATGTTGTTACAGACAAACTGAACTATGGGGCCATGCGCATGTGGTTCTTGCTCAACCCCCCCGGTGCTGCTACCATCC

upper sequence: GRMZM2G147145_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S128_25V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------gttagtttaatgca----tcttcaag----ctggaaatatgatctctt-cat-tgtttgtaccattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
                                                                ||  ||||| ||     || | |||    |||   | ||||  |  |  || || | |     |  |  | ||  | |||  | || | |||||    |         ||||||||||| || ||||| || |||||  ||||||| ||||| || || ||||| |||||||  |||||||||||    ||||| || |||| |||    || |
gtatggagtctatcaagatctattcttttctgatagaggcctatggcctcagatattctatgttttgttttaaagcgacgctcgttaagtatgctgctgaaatgacttggtatatatgatcgagttttccatggatctgtcatagcaaacacctatttcaactttatctttcttgcagGAGCCAGAGAAACACGTTTTTCACATTGTTACCGACAAGCTAAATTTTGGTGCCATGATGATGTGGTTTTTAGCAAATCCTCCCGGGGCTGCTGTCATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattgactggtcaattatattacactcttatttttcttgctataaatttgcagGAGCCTGAAAAACATGTATTTCATCTTGTTACTGACAAACTGAACTTTGGGGCCATGAACATGTGGTTTTTGCTGAATCCACCTGGGGATGCAACAATCC
  cattgac  putative branch site (score: 3)
              aattatattacactct  TA-rich tract