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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC

Basic information

species Zea mays
transcript GRMZM2G057576_T01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
------------------------gtttgaattctttattcctggggtctgcaaagtgac---aagtttcacattccctttttaa-gtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
                         ||  |   |   |||   ||  | |||| |   ||   ||  |   | ||    ||||   |  || | ||||| ||  | |   | | ||||||||||||||||| |||| || ||||| ||||||||  ||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||| |||
gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
------------------gtttgaattcttta------ttcctggggtctgcaaagtgaca-agtttcacattccctttttaagt---ggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
                    ||| ||||   |      ||   ||  | |||| |   ||| |     |   |   || ||  ||    |||| ||||| ||  | |   | | ||||||||||||||||| |||| || ||||| ||||||||  ||||||| || |||||||||||||| ||||| |||||||||||||| ||||||||||| |||
gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatctcatcttttatatttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 22
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
          |   |  ||      | ||     ||     |  |||| || | || | |   || ||| |  ||   ||||  ||   |||| || || || ||||| |||||||||||||||||||| || |||||||| ||||| ||||| ||||| || ||||| || || |||||||| || |||
---------gtgcgtctctctatctttcatctccac-----tatcattgccatgttcatt---tctcatttaattttttatgcata---gGAATCGTCTCCGCTTGCTCACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 21
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
    | | | | | |||       || ||          |||     || | |||    |   ||     |  |||   |||     |||||| || || || |||||||| || || ||||| ||||| || ||||| || ||||| ||||| ||||| |||||||| || || ||||||||||| || 
----gtagtatcttttctctaatcctacat-----ttctttttgtgctcgcatttctgattattccgtggtacttgg-catg-----cagGAATCGGCTTCGTTTGCTTACACAGTTTTTGGAACATCTTGTAAGTGAGGGAAGCCAGGATGTACATGTTCACAATGCACTGGGTAAAATCATCATTGAT

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
--gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
  ||   | || |||   ||  |  ||  |||| |         || |||   ||||        |||  ||  |||  ||  |     ||| || || || || ||||||||||| || ||||||||||| || ||||| || ||||| ||||||||||| || |||||||| || ||||| ||||| |||
gtgtgcaagttttttccaccctgcatccccaaatta-------ccatattattttttc-------tcatttcactttctatgcg-----cagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 20
--gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
  ||   | || |||   ||  |  ||  |||| |  ||  ||    |||   | |        ||  ||  |  |     ||| |   ||| || || || || ||||||||||| || ||||||||||| || ||||| || ||||| ||||||||||| || |||||||| || ||||| ||||| |||
gtgtgcaagttttttccaccctgcatccccaaattaccatatt----attttttctc-------attgcactttct-----atgcg---cagAAATCGTCTTCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTACATAATGCTCTGGGTAAAATTATCATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 22
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
   ||   |  || |  ||    | ||||   |  | ||| ||    |  || | |   |   |||  |   |||   | | || || ||||| || || || |||||||||||||||||||||||||| || |||||||| ||||| ||||| ||||| || ||||| || || |||||||| || |||
--gtgtgctagttttctctctattttgca---tctccagtatcg---ttgctatgttcatttctcatgttctttt---tttatgcat-agGAATCGTCTCCGATTGCTTACTCAATTCTTGGAGCATCTTGTAAGTGAAGGAAGCCAGGATGTACATGTACATAATGCCCTGGGTAAAATCATTATTGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 22
gtttgaattcttt--attcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
   ||||| ||||   |      ||| |||   ||    | ||     |      ||   |    ||  || |||||     | |   |||| || || || ||  | || ||||| |||||||||||| |||| ||||| || |||||||||||||||||||| |||||  | || ||||| ||||| |||
--gtgaatccttttggtcatcctggtttgc---gttcataattatgtctgtttagttctggaaactctaatatgtttctgctttt---tcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATTTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
gtttgaattcttt--attcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
||  |||  ||||      || |  | |      | | | || |   |||   || || ||  | ||  || ||| |   | |   | |||| || || || ||  | || ||||| ||||||||||||||||| ||||| || |||||||||||||||||||| |||||  | || ||||| ||||| |||
gtgcgaacccttttagcatcttgaattt---cgttcatatgtatgctattttgttctttag--gctctaatatgtatatgtct---tctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 22
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
   || ||| ||| | |||| |  | |         |  |||   |||  ||| ||   |   |   |||  ||||  | |   |  ||| || || || || || || ||||| |||||||||||||| |||||||| |||||||| ||||||||||| || |||||||| || ||||||||||| |||
--gtgcattgtttttacctgtgtaccgtttccattaatatttttaatt--cttattgctttcgttttatcattttgtgttttgtttgcagAAATCGTCTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGTAGCCAGGATGTGCATGTTCATAATGCTCTGGGTAAAATCATCATAGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 22
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctg-tttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
       |  | | | |||    | |||   ||  |  |||   || |  |||||||  |  ||  | | || |||| || ||  | |||| || || || || || || ||||| |||||||||||||| |||||||| || |||||||||||||||||||| |||||||| || |||||||| || |||
------gtgatgtgtccctaccatatgccctgtt-cgggtt---cactttctttttacttcaattgcttatgctttgcatgtggttttcagAAATCGACTCCGTTTACTCACTCAGTTCTTGGAGCATCTTGTGAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCTCTGGGTAAAATCATTATAGAC

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
------------gtttgaattctttatt-cctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
            | |||  || || | |  ||      |  |  || || | ||  |||| |     |      || |  ||  |||      | | ||   |||| || || ||  || | || |||||||| |||||| | || |||||||||||||||||||||||||| ||||||||||||||||| |||||||| || 
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttata---gGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT

upper sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctg--tttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
                                        |     |    |||| | ||   |||    ||   || | | | | |  ||| || || ||  |  | || ||||| || |||||||| || || || |||||||||||||| |||||||| |||||||| || || ||||| |||||||| 
---------------------------------------gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC
                tttttaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctgtttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG