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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC

Basic information

species Zea mays
transcript GRMZM2G059624_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgca-gtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                 ||| || |   |||   |||   |     |  | ||      |||||     | | ||  | || | ||     | ||||    || |      ||  |||| ||||| | |||||||||||| ||||| ||||| |||||||||||  |||| || | ||| |||||||||||||| || ||| | ||||| ||||||    
-----------------cta-acctatctgtgattaaactttatgttgccgttattctcttgtatgcatatggtttctcctgt-ttgcccctaaactttggttgctcaaa-atgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgca-gtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                 |||  |  |||    |  |||| ||  |    | ||      |||| |    | | ||  | || | ||     | ||||    || |      | || ||| ||||||| |||||||||||| ||||| ||||| |||||||||||  |||| || | ||| |||||||||||||| || ||| | ||||| ||||||    
-----------------ctaacctatctgtgattaaactttatgttgtccgttattctcttgtgcgcatatggtttctcctgt-ttgcccctaaactttgattgctcaa--aatgcgcagTTTGGTTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactata--gatctagcattgagtatttgtacatgcagtttgattctata-ttataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                     | |||      |  |||||||  |||     | |  ||  |  |  || ||  | | | ||  | ||||   ||| ||     |   |    ||| |||| ||||| | |||||| ||||| ||||| || ||||||||||||||| ||||||| | ||| || ||||||||||| || || || ||||| ||||||    
---------------------agattaac-cattgaactatactgattggttactctgttatgttgaatacaaatggttcctccacttatcccttaccttttgatttatactaattttgcagTTTGGGTATATTGTATTGACTACCTCTGCCGGCATCATGGATCACGAAGAAGCTAGGAGAAAAAATGTTGGTGGTAAGGTACTGGGTTTCTTCTACTAGA

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagc--attgagtatttgtacatgcagtttgattctatat-tataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                     | |||      |  |||||||    |||   | |  ||  |  |  || ||  | | | ||  |  |||   |||  |     |   ||   ||| |||| ||||| | |||||| ||||| ||||| |||||||||||||||||  |||| || | |||||| ||||||||||| || ||  | || || ||||||    
---------------------agattaac-cattgaactatattgatagtttactctgttatgttgaatacaaatggttcctccacctatcccttacattttgatttatggtaattatgcagTTTGGGTATATTGTATTGACTACCTCTGCTGGCATCATGGATCATGAAGAGGCTAGGAGGAAAAATGTTGGTGGTAAGGTATTGGGCTTCTTCTACTAGT

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G10950.1 (Glycine max), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC
             |  |||         | |    || | |  |   |   |  ||  ||||||||     ||  ||| |  |   |||  |   | | || | |     ||  |||| ||||| | |||||| ||||| ||||| |||||||||||||||||  ||||||| | ||| ||||||||||                          
-----------attaagctg-gtgcctgtatcctaaattttttaatcatggtataggctttgtacaca-gtttccattgttgaccctaacct---ttgtttacacaa---atgttgcagTTTGGGTATATTGTGTTGACTACCTCAGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAGAATGTTG--------------------------

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G00590.1 (Glycine max), 3'ss of exon 2
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgca-gtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                   ||  ||   || ||  |||| ||  |    | ||      |||||     | | ||  | || | ||     | ||||    || |      ||  |||| ||||| | |||||||||||| ||||| ||||| |||||||||||  |||| || | ||| |||||||||||||| || ||| | ||||| ||||||    
-----------------taacctatctgtgatta-aactttatgttgtccgttattctcttgtatgcatatggtttctcctgt-ttgcccctaaactttggttgctcaaa-atgatgcagTTTGGGTATATTGTCTTGACAACCTCTGCTGGTATCATGGATCATGAAGAGGCTAGGAGAAAGAATGTTGGTGGTAAAGTGTTGGGTTTCTTCTACTAGG

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------gtacgtccgttccttcgctacac-attcttgtt----tctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                                                |   || | | | |  ||   |  ||| | ||    | ||| |  |  | |||  |  | || ||   | | |  | |  ||| || ||| || || | |      | ||   |  |||||| |||||||| |||||  |||| ||||| || || |||||||||||  ||||||| | ||| ||||| |||||||| || || || || || || |||    
gttagtctagagactatatagtagtggtaccaatcaatgttttagctattgatctgctgccttactttgctgttcctattatggtttaattggatgtttagtgtc-attactttgccttactttatctttcaatgttacaacttcattgaa---cacttctctatgtgcagTTTGGTTTCATTGTTCTGACGACCTCAGCGGGAATCATGGATCATGAAGAAGCTAGGAGAAAGAACGTTGGTGGCAAAGTTCTTGGGTTCTTTTACTGAA

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
    ||| ||   ||   | |   ||| | ||| |   | | | | |   |  ||| | |  || || |||  ||||  || |||           || | |     |  |||||||| ||||| |  |||||  | || ||||||||||| || ||||| ||| ||||||||| ||| |||||||||||||| || || || || || || |||    
----gtctgtcttttaagt-cttgttcatattt-tggttct-ggttttttaaagagcaatcttatattcag--tgatcttacattg----------agttct-----taaattgtgcagTTTGGGTACATTGTTCTTACGACCTCGGCTGGTATTATGGACCACGAAGAAGCCAGGAGAAAGAATGTTGGTGGCAAGGTTCTTGGCTTCTTTTACTGAA

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g02460.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtacgtccgttccttcgctacacattct----tgtttctaactatagatctagcattgagtatttgtacatgcagtttgattcta-tattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                |     ||  ||    | | |        || |  |||  ||  |  | |||    | |   |  ||  || | |  ||  | ||| ||   ||     |  |     || |  | |||| ||||| | |||||||||||| || || |||||||||||||||||  ||||||| | ||| || ||||||||||| || || || ||||| || |||    
gttggcatccaaaacccactattttttttataaaaaaaaaaaaaatgatcttaaaaatgaacttggcaaactgcaaggggccaatcattattctttgagtatgatttcttggggtgactaatgagtgctatttgcagTTTGGATATATTGTCTTGACAACTTCTGCTGGCATCATGGATCATGAAGAAGCTAGGAGAAAAAATGTTGGTGGCAAAGTTCTTGGTTTCTTTTACTAGT

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 4
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
         |   || ||| || | |  ||| |   |   ||||| |  | ||    |    || |||  |||| |||  ||     |  ||   |     |||          |||| ||||| |  |||||  |||| || ||||||||||||||||||||  | || || | ||| |||||||||||||| || ||||| ||||| ||||||    
---------tattttagctgcatactagtgtattacaggctagattt--cctttgccaacaatatatgtggtttcatttgatg----acctttgatgatggtccaaaaat----tgcagTTTGGATACATTGTGCTGACTACTTCGGCTGGCATCATGGATCATGAGGAGGCTAGGAGAAAGAATGTTGGTGGCAAAGTGCTTGGTTTCTTCTACTAGG

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S41_94V6.2 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------gtacgtcc--gttccttcgctacacattcttgtttctaactatagatctagcattgag----tatttgtacatgcagtttgattctata------ttataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                                                      ||||      || |  | |  | |  ||   |  | | ||  | |    | | | |      | ||| |   | |  || || ||  |       | ||   |||  |   |||   | |    |||||| || || |  ||||| |||||||| |||||||| |||||||||||| | ||||| | |||||| ||||| || || || ||  | || || || |||    
gttattatttaccacctgtcatcgtggtctactcaatattattcaaaatcggtggtacaatgtggtgctgtggagatagcttaacgcatgtgacggttgcgtcatcctagtacttctctttttttcttcgtttagagtcggtggaatcttcattccttatatgtattttatttttgcctgtgcagTTCGGATACATTGTTTTGACCACTTCGGCTGGAATCATGGATCACGACGAAGCTAGGAGGAAAAATGTCGGAGGCAAGGTTTTGGGATTCTTTTACTAGT

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaacta--gctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                     ||  ||  |  |  | |         || |||   | ||    | |||  || | |   |   |  ||| | | |   |  ||     ||  || |||| ||||| |  ||||| ||||||||||| |||||||||||||| ||| | || || |  |||||||||||||| ||||| || || ||||| || |||    
--------------------aacgatcaagcgttaatcctcctcaagaggatttcatgttaccgc-tgcttttaggtatgaacctgaaatctgattgttgagtttttcatcttttttgcagTTTGGATACATTGTTTTGACCACCTCAGCTGGCATCATGGACCACGACGAGGCTAGAAGGAAGAATGTTGGAGGAAAGGTCCTTGGTTTCTTTTACTGAG

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14550 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                                            | |    ||||| |   | |      | ||| | | |     |||    | |  || | |   ||  | |  || |||||||  |||||  |||| || ||| | || |||||||||||| | ||||| | |||||||||||||||||| || || || || || |||||     
-------------------------------------------gtttgattttgag-agacgaatcgatggcttggtgcaaagaagtaa--cgattttctcttcg-atctctggctcagTTTGGTTACATTGTGCTGACAACATCGTCCGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT

upper sequence: GRMZM2G059624_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26253 (Selaginella moellendorffii), 3'ss of exon 2
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC----
                                            | |    ||||| |   | |      | ||| | | |     |||    | |  || | |   ||  | |  || ||||| |  |||||  |||| || ||| |||| |||||||||||| | ||||| | |||||||||||||||||| || || || || || |||||     
-------------------------------------------gtttgattttgag-agacgaatcgatggcttggtgcaaagaactaa--cgattttctcttcg-atctctggctcagTTTGGCTACATTGTGCTGACAACATCGTCTGGTATCATGGATCACGACGAAGCGAGGAGGAAGAATGTTGGTGGCAAGGTCCTCGGCTTCTTCTATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC
                            atttaac  putative branch site (score: 3)
                                      ctttccctgtccatt  putative PPT
         agtttgattctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtccgttccttcgctacacattcttgtttctaactatagatctagcattgagtatttgtacatgcagtttgattctatattataatttaactagctttccctgtccattgtGCAATTTGGTTTTATTGTCTTGACCACCTCGGCTGGCATCATGGATCACAAAGAAGCCACGAGGAAGAATGTTGGTGGAAATGTGCTAGGTTTTTTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA