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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca...

Basic information

species Zea mays
transcript GRMZM2G430947_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G06720.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgt--tcgttatttggttttattgattct---gttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca--------------
|||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| ||||  |||||||| || ||||||||  |  || | | ||||  | || ||       |   | |||||| | | | |     |  |    || ||| ||  |||   || | | |    |    ||                
TGCATTGAAAATTTATATTAAAGCTAGAGCCACACCAAAAGTTGTTGCAGCTTTTGCGGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgtattttttttctagtttagtagaatcataaaaatattggtgttgtgattaaatgtttttaaattagttttttttaatactatctttctgatatattcttttcttttcctttgatgaag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcg---ttatttggttttat------tgattctgttttcagttgttgtaactcatttgagcttcacattttat-ttctacaacttggttccaggttgggtacactcca
|||  | ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||||||||||||||  || |||||||| ||||||||      || |||  || | |      | || ||| |||  |||  |   | |  |||| ||||| | | |||  ||||  ||  | |||      |            
TGCTTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTAATATACTCTAAGCAGgtagaggcttgtttatttatgtatcaaataatactgatttttgttcatcagattgttttgtgcttctcttgttaaattctttaatattgttatgacctat----------

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttc----gttatttggttttattgattctgtttt------cagttgttgtaactcatttgagcttcacattttatttctacaacttggttccag-gttgggtacactcca----------------------------------------
 ||| |||||||||  || || || || || || || ||||||||||| || |||||||| |||||||| ||||||||||  ||||||||||||||||||||         ||||  || |   | || | ||||      || |     ||       |  |  | | |||||  |   |  || |  |   |   ||   |    |  |                                        
CGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTCTGATATACTCAAAGCAGgtaatgaaacaatttttttattaggcttttattttatagaacaataaaaatagtggtactatgagttatattttggtctcattacataatctaatcattttttgttttatagtagatgttaaatgtattttttcccttttatttgctgaag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA01G38580.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgtt----ttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca-------------------
|||| ||||||| || || || ||||| || || || ||||||||||| |||||||| || |||||||| ||||| ||||  |||||||| || ||||||||   || |||   |||| |       |     | | | |||||| | | | |     || | ||||  ||| |  ||     |     ||  | | || ||                     
TGCATTGAAAATTTATATCAAAGCTAGAGCCACACCGAAAGTTGTTGCAGCTTTTGCAGAGAGGAGGGAATTTGATAAGATCCTGATATATTCTAAGCAGgtattttgttttagtttagtagaatcataaaaatgctggtgttgtgattaaat--gtttttaaatttgttttttttaatactatc---agtctgatgcattcttttcttttcctttgatgaag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G37510.1 (Glycine max), 5'ss of exon 12
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggtttt--att-gattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca
|||| |||||||||  || || || || || || || |||||||| || || |||||||| |||||||| ||||||||||  ||||||||||||||||||||     |     ||||  ||| |  | | ||||         |||   | | |   |     || |||||      ||   | |    |    ||   |   
TGCATTGAAAATATTTATCAAAGCCAGAGCCACACCGAAAGTTGTGGCAGCATTTGCTGAGAGGAGGGAATTTGACAAGATTCTGATATACTCAAAGCAGgtaatgaaacaaattttttattaggctttattttatagaaccataaaatagtagtaatatgagttatattttggt--ctcattacataatctaataattttt-

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G06340.2 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgt-------tatttggttttattgattctgttttca----gttgttgtaactcatttgagcttcacattttatttctacaacttg---gttccaggttgggtacactcca-----------------------------------------------------------
|||  | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| |  ||||| ||||| || ||||| | |       |||       ||||||  ||   | ||     |  || |||  |  ||  |      ||   ||||   | || ||     |     |||  |  | | ||                                                           
TGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCGTTTGCTGAGAGGAGGGAGTTTGACAAAATTCTGATTTACTCTAAACAGgtgcctgtttacttatcaaagaatattgaagcttaatccatagaataattttaatgctattatggcatgtatagcattttgtctacctgtataattatcattgcatgtattgcactttcattttactgtaaacatttggtcctgaacattgtattacttatttgttgctatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgt-------tatttggttttattga--ttctgttttcagt-tgttgtaactcatttgagcttcacattttatttctacaacttg---gttccaggttgggtacactcca-----------------------------------------------------------
|||  | |||||||| || || || || || || || |||||||||||||| |||||||| ||||||||||||||||| |  ||||| ||||| || ||||| | |       |||       ||||||  ||   |    ||  |  | ||   |  ||  |     |||   ||||   || | ||     |     |||  |  | | |                                                            
TGCTTTAAAAATATATATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCATTTGCTGAGAGGAGGGAGTTTGACAAAATTCTGATTTACTCTAAACAGgtgcctgcttacttatcaaagaatattgaagtttaatccatagaataatttagtgctattatggcatgcatagcattttgtcaccctgtataattataattgcatgtattgccctttcattttactgtaaacgtttggtcctgaacattgtattacttatttgttgctatag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcg---ttatttggtttt--attgattctgttttcagttgttgtaactcatttgagcttcacattttat-ttctacaacttggttccaggttgggtacactcca--------------------------------------------------------------------------------------------
|||  | ||||||||||| || || || || || || ||||||||||||||||||||||| || ||||||||||||||||  ||||||||||| ||||||||      || |||   | |  | | || ||| |||  |||  | | | || |||| ||||| | | |||  ||||  ||  | |||      |    |   |  |                                                                                            
TGCCTTAAAAATATACATCAAAGCCAGAGCTACTCCAAAAGTTGTTGCTGCTTTTGCTGAGAGAAGGGAGTTTGACAAGATTCTGATATACTCTAAGCAGgtagaagcttgtttatgtatcaaataatactgatttttgttcatctgattcttttgtgcttctcttgttaaattctttaatattgttatgacctatagaggttttaattggcctgtataattaacattgcatatcttgcctttgcattttactggaacaaattgtggctgatcattttcattactttttccgctacag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcac-attttatttctacaacttggttccaggttgggtacactcca-
||| || ||||||||||| || ||||| || || || ||||| ||||| |||||||| ||  | |||||||||||||| | | |||| || |||||||||||     |||  ||||||  | ||      || |||||| |   |    | |   |||   |  |        | | | |||  | |||| |   |||| | 
TGCTCTAAAAATATACATCAAAGCTAGAGCTACTCCAAAAGTCGTTGCAGCTTTTGCAGAGCGAAGGGAGTTTGACAAAATATTGATTTATTCAAAGCAGgtaaacaattaagttttaaagtttgccccctccgttgttatgtttaccctaaaggtcattgtgctcaagaggtaccattgttttatgttgtg---actctag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca-
 || |||||||||||||| || ||| |||| || || |||||||| || |||||||| ||||| |||||||||||||| | |||||| ||||||||||||||  |  ||  | | |     ||    | |||  || || | || |  |  || |      | |  |     | | | ||| ||  ||| |   ||| || 
CGCTCTGAAAATATACATCAAAGCTCGGGCGACTCCAAAAGTTGTAGCAGCTTTTGCAGAAAGAAGGGAGTTTGACAAAATACTGATTTACTCAAAGCAGgtaagcaataagatctatagtataacctcttctattatttttaccc--taaagttctgttgtctcatgaattaccattgtttcatattgtg---acttcag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca--------------------------------------------------------------------
|||||| |||||||| || || || || ||||| || ||||||||||| || ||||||||  |  ||||||||||||| |  ||||||||||||||||||||   |    || | |    | ||  |||  |  ||     ||   || ||   ||    ||||   | || || ||| |||     ||     |||                                                                       
TGCACTCAAAATATATATTAAAGCGAGAGCAACTCCGAAAGTTGTTGCAGCCTTTGCTGAGCGTCGGGAGTTTGACAAAATTCTGATATACTCAAAGCAGgtgaatagcatgatctag--gttttcgttgcctcttaa-acaaaatatatgttttttttctttttcctgtaaaatttgtttcttatctgttactactttttttatcagtaatattttattattgaattatgggcatttagagtaactgtgttttcttcgtcgctgtag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 5'ss of exon 13
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgt-tatttggttttattgattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggt--tccagg---ttgggtacactcca----------------------------------------------------------------------------------------------
||||||||||||||| || || |||||||| || || ||||||||||| || |||||||| ||||||||||| || || |  || |||||||| ||||||||   | ||||| || || ||     |   |  |  | ||  |  | ||||     ||| | | |||| ||| | | | ||  |   ||   ||    | | |  |                                                                                              
TGCACTGAAAATATATATCAAAGCTAGGGCCACTCCAAAAGTTGTTGCAGCATTTGCTGAGAGGAGGGAGTTCGATAAAATTCTAATATACTCCAAGCAGgtatatatattttgtattctttcaattacctaaatctttttaagattattttc-tgtcaaaatctattactaaatcatagtagtttgggaattttatcatattatatagcacaatgcatatactatctatgcccttatcattattttttattgctattctttgaatggtctttgtacttctgattttttcatctatgcag

upper sequence: GRMZM2G430947_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 5'ss of exon 14
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttat-ttggttttattgattctgttttcagttgttgtaactcatttgagcttc----acattttatttctaca-acttggttccaggttgggtacactcca-----------------------------------------------------
 ||  ||||||| ||||||||||| ||||| || || || || ||||| |||||||||||  || | |||||||| ||||  ||||| ||||| ||||||||| || ||  |     ||||   |   | ||    | |   |||    ||    | |     ||||  |||||     | |   || |   |    |     |                                                       
GGCTTTGAAAATTTACATAAAGGCCAGGGCTACACCCAAGGTGGTTGCAGCTTTTGCTGAGCGGCGAGAGTTTGATAAGATTCTGATTTACTCCAAGCAGgttagtcatgctcaaaatatttgatggctcttggcctttcacaacgtgctttgtttcctttggcattgcatttcagggtattcaattgcctttcttctttgtgcgggggagcaaacctacacacgtgtattgtttgacgcagtttttcctacactgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCACTGAAAATATACATAAAGGCTAGGGCAACCCCTAAAGTTGTTGCTGCTTTTGCTGAAAGGAGGGAGTTTGACAAGACACTGATATACTCAAAGCAGgttcgttatttggttttattgattctgttttcagttgttgtaactcatttgagcttcacattttatttctacaacttggttccaggttgggtacactcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG