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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC

Basic information

species Zea mays
transcript GRMZM2G155837_T02
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 3'ss of exon 20
-------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
        | ||     | |||| |  | |   |    |   | ||  ||   |  | |    |   |    || ||| |||| | |  |||  ||| |   |||||||||| |||  |||||||||||| ||||| || || ||| ||||| ||||||||||||| |||||| ||||||||||| | |||||||||||||| || |
tgaataaaccagaaaaaaatata-tgccaatgtatccattacagaagatgtccggcattgcaatacttg---aatcttgcattttggtgaattccactt---tgcagGGTAAGTTAAATGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGAAAAAAGCAATTTGCAACGGAAATAGAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52606.1 (Oryza sativa), 3'ss of exon 6
------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
      || | || | |     |||  |  | |    |   ||||   |  ||  | |    |  ||    |||||| |||| |||   |  |  ||  |||||||||||| ||| ||||||||||||| ||||| || || ||| ||||| ||||||||||||| || |||  |||||||||||| |||||| ||||||| || |
accgtatcca-ttacaaaagatgttcttttagaaacattacaaaagacgtttgacattgcagtacctg---aaacttgcatttttggtga--atgccaccttgcagGGTAAGTTAACTGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAGTGCAATTTGCAGCTGAAATACAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 3'ss of exon 18
-------tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
       |  | | |  | |||| || | |   |    |   ||||  ||     ||||       ||    |||||| |||| | |  |||   |||    |||||||||| ||| ||||||||||||| ||||| ||||||||| ||||| | |||||| |||| || ||||| ||||||||  | |||||||||||||| ||||
ttattaataaattggaaaatata-ttccaatgaatccattacaaaagatgttcagtactgcaaaacctg---aaacttgcattttggtgaattctacca---tgcagGGTAAGTTAACTGATGGAAGGGTAGTGGCAGTAAAACAGCTATCTCAGACATCTAATCAAGGGAAACAACAATTTGCGACTGAAATAGAAACTATATCTC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 3'ss of exon 16
tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattc---aaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
||        |  |   || | |   |    |    |||| ||   |    |    || | || |    ||||| |  | | |  |||| |||||   ||||||| || ||| ||||||||||||| ||||| || || ||| ||||| ||||||||||||| || ||| | ||||||||  | || ||||||||||| || |
tcagaaaaaaaaaaacattccaatgtatccattaccaaatatgttcggctttgacattgcgatcccttgaacttgctgtttggtgaatgccacct---tgcagGGCAAGTTAACTGATGGAAGGGTAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTTGCGACGGAGATAGAAACTATATCCC

upper sequence: GRMZM2G155837_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os04g52640.2 (Oryza sativa), 3'ss of exon 19
-tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttcta-----ttcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
  | |  |  ||    || || ||   |  |||  | ||||   |  | || |     ||  |     || || ||  |||| | |  ||||  ||||   ||||||||||  ||   ||||||||| | ||||| || || ||| ||||| ||||||||||||| || ||| | ||||| ||| | |||||||||||||| || |
gacca--taataggtgaggttttatg-aaatttactcaaataaaaaagatattcagcattgcaaatacttgaagctggcattttggtgaatgcaacct---tgcagGGTAAGCTAATGGATGGAAGGATAGTGGCAGTGAAGCAGCTATCTCAAACATCTCATCAAGGGAAAAAACAATTCGCAACTGAAATAGAAACTATATCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC
                     aacttac  putative branch site (score: 2)
                                            cctgctt  putative PPT
      ttttttttctattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctagttgctattatagtttctacacaggtttggtaaaatgtgagtgctacttttttttctattcaaacttacattgttgaaaatgacacctgcttgcagGGTAAATTAGCTGATGGAAGGGTGGTGGCTGTAAAACAGTTATCTGAAACATCTCATCAGGGAAAACAGCAATTTGCAGCCGAAATAGAAACTATTTCTC

- -agttgct
- - - - - - - - - - ctacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa