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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG

Basic information

species Zea mays
transcript GRMZM2G014805_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
       |||||||| ||| |  |   |    |||| | | |||||| |||||| | || ||| | | || | ||| |    ||||  ||| || | || |||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||
tattgtgttgttaatatagcattactctg---acttgaaagtgatgtagtgatgcttttcccatgattaacactctgagctatttggcatttttatgctgcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACACATTGACAAGAAACTAACTTTCCGTTCCAGTCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 11
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgat---ctttccaagttgaatattctaatgcttttgaaattctt-gttctt-cagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
     | | |     |||   | ||    ||||| || |  | |  ||||  |   ||||    | || |  |  |||       ||  || || ||| ||  |||||||||||||||| |||||||| ||||| |||| ||||||||||||| | || || ||  | || |||
----atatgagccctgtatcgt-ttccatacttactattctttttctgatcttagactttgagggatgcaattagtaaattgaccgagcttttttgtttttgtagGAAATTAAGTTTGAACCAAATGTCATGTGTGAACCTATTGACAAGAAAGTAACATTTCGAACAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcacttaat--aatga-tgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
    | ||| ||| | |  | ||   ||| |  ||||    ||||| || | |||  ||| |      ||    | | || ||    |   | | || || | |||||||||||||||||||||||||| ||||| |||| |||||| |||||| | || || ||  | || |||
ttttttatttttattttttt-catctttaggttcttatctcaatgaatgacttga--atcgtgtggcatttgtgaatttactgtgcct---actattattgtgcagGAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCTATTGATAAGAAAGTAACATTTCGAGCAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 19
---gtcattgttaatgtagtacaatgttatgcactta-ataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
   | | || ||  | |  | ||   |||    || |  | |    ||       ||| |      |||   | |  | ||    |   | | || || | |||||||||||||||||||||||||| ||||| ||||  ||||| |||||||| || || ||  | || |||
aaggaccttcttt-tatttttcatctttagtttctgatgtgaacgagtgacttgaatcgtgtggcattggtgaattaactgtgcct---actattattgtgcagGAAATTAAGTTTGAGCCAAATGTTATGTGTGAACCCATTGATAAGAAACTAACATTTCGAGCAAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: PP1S123_138V6.1 (Physcomitrella patens), 3'ss of exon 19
-------------------------------------------------------------------------------------gtcattgttaatgtagtacaatgttatgcacttaataatgatg--tcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                                                                                          |||  |   |  ||||    ||| |  | |  || |||  ||   |  || ||  | ||||| ||  |   ||    |  |    ||     | |||||||| ||||||||||| ||||| |||||||| || ||||| |||||    ||||||    |||| |||
gtataatgactcagtagtttgatgaagtttgtaatttctcactctcttctggatgttctaaaacttgaccttctatttatttgaaaaaggtgtccacaaataacaacacaatgaatgtgaggattatgagtcagcactattttcgccagttggatcattctatctaatccatgcactaagcttgcagGAAATCAAGTTTGAGCCGAATGTCATGTGCGAGCACATTGAAAAGAAGTCCACTTTCAAGGCTAGCCAG

upper sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 19
lower sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 16
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgt-gatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                                             || ||| || |||  |  ||  |||||    |||||     ||| || |||  ||||||||||| ||||| || ||||||||||||||||  ||||||||||||||||| || ||    ||||||
---------------------------------------------gtagataatgttttta--ttctatattgatttgcttc-atcattgtt-ttcgacagGAAATTAAATTTGACCCGAATGTGATGTGCGAACCAATTGACAAGAAACTTACGTTTCGAGACAGTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG
                        ttctaat  putative branch site (score: 2)
                                         ttcttgttcttc  putative PPT
                 ttgaatattctaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcattgttaatgtagtacaatgttatgcacttaataatgatgtcgtgatgatctttccaagttgaatattctaatgcttttgaaattcttgttcttcagGAAATTAAGTTTGAGCCAAATGTGATGTGCGAACATATTGACAAGAAACTTACTTTCCGTTCTAGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA