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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

Basic information

species Zea mays
transcript GRMZM2G466136_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g40180.1 (Oryza sativa), 3'ss of exon 2
agtatgctatgttaggcttgtttactttattttatta---ttgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
 |  ||||    |    ||    | ||||| | || |   ||| |  ||  || |     |||  || || |       ||| |||| || |  | || |||||||||||| || |||| |||||||||||| ||||||||||||||||||||  |||||||| |||||||||| |||||||| |||||||||||||||||||
-gggtgctcccatttatttaccaa-tttatataatcacatttgaatattttgtcctgtaatcaaaatattgtgcttaactat-ttgtcgttacctttcctcagGGTTATGTGGTTTACCGTGTCCGTGTGAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTACGGCAAGCCCAAGCACCAGGGTATCACCC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g19370.1 (Oryza sativa), 3'ss of exon 2
-agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatg-tcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
    |   | | ||    |  |    | |  || | | ||| |  ||  |  |||||  ||   || || |       ||| || ||     ||   ||||||| ||||| || |||| ||| || || || ||||||||||||||||||||  |||||||| ||||||||||||||||||| |||||||||||||| ||||
agccaaaatgtattcacatgctgctgtctgattcacttttgaatgttttggccctataatccaaatattgtgcataactattttttgac--cttgctttcagGGCTATGTGGTTTACCGTGTTCGCGTCAGGCGTGGTGGCAGGAAGAGGCCAGTGCCCAAGGGTATTGTCTATGGCAAGCCCAAGCACCAGGGTATTACCC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G16720.1 (Arabidopsis thaliana), 3'ss of exon 2
------agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
       |     ||||  ||  ||||||  |  |||  || |||     |  ||| |  |  |  || |   | |  | |||  | |||  | || ||| | ||||| | ||||||||||| ||| |||||||||||||||||  | ||||||||  |||| ||| ||||||| ||||| |||||||   |||||||  | || |
gttagtggagaaatatggaagcgttgtttgatg-attgaatcatttttaatctagt-ctcaaattctgttacaaatcta-gttgagatgt--tgatgtatgt-cagGGCTTTGTTGTGTACCGTGTACGTGTGAGACGTGGTGGACGCAAGAGGCCAGTGCCTAAGGGTATTGTGTATGGTAAGCCAACAAACCAGGGAGTGACAC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0551g00020.t01 (Vitis vinifera), 3'ss of exon 2
---agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
   | |   || | |    |  |||    |  || || | |   ||  ||        ||  || || |      |||  |   || | |    | | |||||||||||||  | || | ||| ||||| |||||||||||  ||||||||||| |||||||| | ||||| ||||| ||||| |   |||| ||| | ||||
tctaat-cactctctcgatccagttctgctgcttgtaatctataagcctggaattggttgctat-atctacacaaatgacactctg-gatgtactgttttcagGGTTATGTGATTTATCGTGTTCGTGTTAGACGTGGTGGTCGGAAGAGGCCTGTGCCCAAGGGAATTGTTTATGGTAAGCCCACAAACCAAGGTGTTACCC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S34_445V6.1 (Physcomitrella patens), 3'ss of exon 2
--agtat-gctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
  |  ||      |  | | ||   || ||    |||  || | | ||   |   | |||  ||  |  | | |||  |    | || ||  | |   || |||||||||| ||||| |  ||||| ||| | ||||| ||||||||||||||  |  ||||| ||||||| ||||| ||||| ||| |||| ||||| || |
tcaacatcagctcgccaaggttaaatattta--cttaacatggtatttgttgattccatgcgattctaat-tctgacatatcatcgttgtggtcttgttttagGGTTATGTGGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCTAAGAACCAAGGTATTACAC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S152_141V6.1 (Physcomitrella patens), 3'ss of exon 2
------agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
      | | |    | |||||     | | ||    || ||  |  | ||  |||   ||   |     |    ||||  |  || |||  | || | | |  |||| ||||| ||||||| |||||| ||  | ||||| ||||||||||||||  || | ||| ||||||| ||||| || || ||| |||||||||| || |
gtcatgactctatctttttagggca--tcatttcgaattcttcata-atttcaagtgtttactcctgttctactcttgacat--tggtgtcattatct-tgtgtagGGATATGTGGTGTACCGTGTCCGCGTTCGCCGTGGAGGCAGGAAGAGGCCAGTGGCGAAGGGTATTGTGTATGGAAAACCTAAGAACCAGGGTATTACAC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S28_15V6.1 (Physcomitrella patens), 3'ss of exon 2
agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacct--atgtcatg-attttatttgatgtta--tgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
    |||  ||| || ||||  ||   ||  || |  |    |||||  | | |  || || ||     || |||  | |   | ||   ||   ||    |||||| || || ||||||| ||| |||||| | ||||| ||||||||||||||| |  | ||| ||||||| || || ||||||||| |||||||||| || |
---ctgc--tgtcagtcttgagtaaaatacattctcttgcttgtttgtctccttcaatttcttgtggggtacttggagctgattatttctgtgtgtttgtatcagGGCTACGTGGTGTACCGTGTTCGTGTGCGCCGTGGAGGCAGGAAGAGGCCTGTTGCTAAGGGTATTGTGTACGGAAAGCCAAAGAACCAGGGTATTACAC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S68_114V6.1 (Physcomitrella patens), 3'ss of exon 2
agtatgctatgttaggcttgtttactttattttattattgcag---tttgagtacc-tatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
   | |    |||  |  |  ||| | |   ||  |   | |    |||| |     |  |    ||   | ||| |  ||||| | |      |||| || |||| ||||||||||| |  ||||| ||| | ||||| ||||||||||||||  |  ||||| ||||||| ||||| ||||| ||| |||| ||||| || |
--cacgtggcgttcagtatagttattgtggattgattcagaaaggatttgtgggttatccgcttcgaagct-tttaacattatgatttatggccttat-tttagGGCTATGTTGTGTATCGCGTCCGCGTGCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAAGGTATTACGC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S134_151V6.1 (Physcomitrella patens), 3'ss of exon 2
agtatgctatgttaggcttgtttactttatt-ttattattgcagtttgagt--acctatgtcatgattttatttgatgttatgtt---gtggtaat-----ttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
           |||  ||| |   |    || || |||  |    | || |  | | || | ||   ||||  ||     || ||    || ||||     | | || ||||| ||||| || |||| |||||||||  | ||||| ||||||||||||||  |  ||||| ||||||| ||||| ||||| ||| |||||||||| || |
-----------ttatacttttcagcacccttgttgttagggtgcctggattctatccatatgatatgtttagatgtctagattttcggatgataatggacctcaactgcagGGATATGTGGTCTACCGTGTCCGTGTCCGCCGTGGAGGCAGGAAGAGGCCAGTTGCCAAGGGTATTGTGTATGGAAAGCCCAAGAACCAGGGTATTACGC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ27946 (Selaginella moellendorffii), 3'ss of exon 2
agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
                                ||  ||| |   ||   | | | |||  |   |   |||||  |  | | ||| |    |     ||||| || ||||| |||| |||||||||| | || || ||| | ||||||||  |  ||||| | ||||||||||| ||||| ||| |||||||||||||||
-------------------------------gtaaaatttctcctttctt-cgtgtgtgctagctc--tttga--tcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTCTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC

upper sequence: GRMZM2G466136_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ36722 (Selaginella moellendorffii), 3'ss of exon 2
agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
                                ||  ||| |   ||   | | | |||  |   |   |||||  |  | | ||| |    |     ||||| || ||||| |||| |||||||||| | || || ||| | ||||||||  |  ||||| | ||||||||||| ||||| ||| |||||||||||||||
-------------------------------gtaaaatttctcctttctt-cgtgtgtgctagctc--tttga--tcgtttcgtgctcgaatcctcacagGGATACGTTGTCTACCGTGTCCGTGTGCGTCGCGGGGGCCGAAAGAGGCCAGTTTCCAAGGGAATTGTCTATGGAAAGCCCAAGAACCAGGGTATCACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC
                      atttgat  putative branch site (score: 5)
                                            tttatcttc  putative PPT
                 attttatttgatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtatgctatgttaggcttgtttactttattttattattgcagtttgagtacctatgtcatgattttatttgatgttatgttgtggtaatttatcttcagGGTTATGTTGTGTACCTTGTCCGTGTGAGACGTGGTGGCAGGAAGAGGCCTTTGCCCAAGTGTATTGTCTATGGCAAGCCAAAGCACCAGGGTATCACCC

-gtatgct
- - - - - - - - cttgttt
- - - - - - - - - - - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttgt