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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgtacgtgtcattttaaagaaatcctctctattaacacttccattttctggtgtcttcaaactgcag

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatt-tctttcatccattattgactgtacgtgtcattttaa-----agaaatcctctctattaacacttccattttctggtgtcttcaaactgcag
 | ||||||||||| ||||| |||||||| || ||||| |||||||| |||||||||||||||||||| | ||||||||||||||| ||||||||||  ||| |     || ||  ||  |  ||  | | | |     ||||||| | |||  | |||| |  |||||    ||  |    | |||||
TTATGTGATCTGTATGAGAACGACTCAATATTTGACAAATTTGAGTGTTGTCTTAGTGGGGATGGACTCCATGTTGCAACTGGTTCATATGGgtattaccttgctcttgttcttagctacatatgaaaatgttatacttagaaatcatgtctgctgacacctt-atttt----tgcatctgtattgcag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G01440.1 (Glycine max), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgta--cgtgtcattttaaagaaatcctctctattaacacttccattt-tctggtgtcttcaaactgcag
|| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| |||||||||||||  |||||   |   | |      |  ||||     ||||||| |  ||     ||   | |||  | ||   ||  | || |  |            
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGTTCTTACAGgtatggatacaaacttaatctatctgtggttctgtcattcttgag----tctgcttcttactattttgtttcatttgataccag----------

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G20830.4 (Glycine max), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgtacgtgtcattttaaagaaatcctctctattaacacttccattttctggtgtcttcaaactgcag
|| |||||| | || || ||||| |||||||| || ||||||||||| ||||| ||||| |||||| | |||||| ||||||| |||||  |||||    ||     |  | | | | ||  |||  || |   |  || || |       || |   | | | | || || |   | | |||
CTTTGTGATTTATATGAAAATGATTCAATTTTTGATAAGTTTGAGTGTTGTCTAAGTGGTGATGGATTGCGTGTTTCAACTGGCTCTTACAGgtatgggatt-----aaaacttaatctatatgtggttct---gttattct-tgagcctgca-tcttactattttgtttcatttgattccag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattg---actgtacgtgtcattttaaagaaatcctctctattaacacttccattt---tctggtgtcttcaaactgcag----------------------------------------------
 | || ||| |||| || ||||| ||||| || |||||||||||||| ||||| ||||| ||||||  ||| |||||||||||||| ||  |||||  ||||  |  ||| |||   |   | | | |  |||        | || ||  || |   |  ||||    |  |  |   ||    ||  |                                              
TTGTGCGATTTGTATGAAAATGATTCAATCTTTGACAAGTTTGAGTGTTGTCTGAGTGGAGATGGAACTCGAGTTGCAACTGGTTCATACAGgtatgccttttttaaatttttgcagaaccttccttttttttcccccttcttctttccttttaggttgtcattaaggttggaagggatctggttgttgaaaccctttggaatgtgcaatactaatactgtttccatggtcccag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatc-cattattgactgta--cgtgtcattt-------taaagaaatcctctctattaacacttccattttctggtgtcttcaaactgcag--------------------------------------------------
|| |  ||| | ||||| |||||||| |||||||||||||||||||| ||||||||||| |||||  | ||||| || |||||||| ||  ||||||   ||     ||   ||   || |  |  ||| ||        | ||  || | |   |   |  ||||   ||   | || ||     | |   |                                                  
CTTTACGATTTATACGAAAATGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCATGCGTGTAGCTACTGGTTCCTACAGgtattgtgttagctacacagtttgatggattcaagtccttgaatgaagtgaatgaaacatacatgacaggactttttttgcgttgtatcacagtattcttgtatgctatgttttatggaggagtatgactgaagtattctctgtgtcgcag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattat-tgactgtacgtgtcattttaaagaaatcctctctattaacacttc--cattttctggtgtcttcaaactgcag-----------------------------------------------------------
|| |||||||| |||||||| ||||| |||||||||||||||||||| ||||||||||| |||||    ||||||||||||||||||||  |||||||  ||  ||    |  |   |  | | ||     | | | |||       ||| | | | |  || | | | || ||| | |  | |                                                             
CTTTGTGATCTCTACGAGAACGACTCTATTTTCGACAAGTTTGAGTGTTGTCTTAGTGGCGATGGCACGCGTGTTGCAACTGGTTCTTACAGgtattttgtttttcagccaaatagttcgatgggtggaacttatggaatatggcacatttagaatgcatcaatgttttgtttctacgatttactttaggacatttttgtgatgtcttgtaaagagattacaactgaactattcctttgtcacag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S425_2V6.3 (Physcomitrella patens), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgta-cgtgtcat-----tttaaagaaatcctctctattaaca-cttccatttt--ctggtgtcttc--aaactgcag----------------------------------------------------
||||||||||| || ||||| || ||||| ||||| ||||||||||| ||| | ||||| |||||  | ||||| ||||||||||| ||  ||||  || ||  ||    |   | | |  | | | ||      |  ||  || | | |  || |  | |||  || |   |   |||||||  | | |   |                                                    
CTCTGTGATCTTTATGAGAACGATTCAATCTTCGATAAGTTTGAGTGTTGTTTCAGTGGCGATGGCATGCGTGTAGCAACTGGTTCCTACAGgtacgtcattgctcagccacatattttggcatcttataagtcctgtaatgaagcatgtgaatcaggaacttgtatctaaacatatgtcttcttagatttttgttagtactcttccaagtgtggtaccgaattgaattattcttctttgtcacag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatt---tctttcatcc--attattgactgtacgtgtcattttaaagaaatcctctctattaacacttccattttctggtg----tcttcaaactgcag------------------------------------------------
|| |||||||| || ||||| ||||| || |||||||||||||| || |||||||||||||||||  | ||||| ||||||||||| ||  ||||||   | | ||| |   ||| ||  || ||       | |  | ||||   |    ||||| ||||  |||      |     || | | | |                                                    
CTTTGTGATCTCTATGAGAACGACTCCATCTTCGACAAGTTTGAATGTTGTCTTAGTGGGGATGGCATGCGTGTGGCAACTGGTTCCTACAGgtattgtatttctcagcttaattgtttgctatattcaatgtctggaggaaagtgtgggaattaagacttgtattggacaatacatctcattagatttttatgatttctcttttaactaagaaaactaatttaagtgtgcttggtacag

upper sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 11
lower sequence: PP1S10_312V6.1 (Physcomitrella patens), 5'ss of exon 11
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgtacgtgtcattttaaa--gaaatcctctctattaacacttccattttctggt--gtcttcaaactgcag-----
|| |||||| | |||||||  |||||||| || ||||||||||||||||| |||||||| ||||| || || ||||| |||||||||||| ||| | |      || |  | | |||    |  |  ||  | |  |   || |  || || | |    ||  ||   ||  ||  |  ||  | ||     
CTTTGTGATTTATACGAGAGCGACTCAATATTTGACAAGTTTGAGTGCTGCCTTAGTGGAGATGGTCTGCGCGTTGCCACTGGTTCTTATAGgtttgttacatttcgaaaaattacttccagcatagttccagaatggggtcgttgctttttaaatgcgcagattagtgtcggttgtttaagcggaggtaga

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71419453|gb|DR804773.1|DR804773
EST:     GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG                         TAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC
genomic: GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttcttt ... caaactgcagTAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC
EST: gi|83278851|gb|DV942859.1|DV942859
EST:     GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG                         TAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC
genomic: GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttcttt ... caaactgcagTAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC
EST: gi|24934367|gb|CA452585.1|CA452585
EST:     GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGG                         TAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC
genomic: GAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttcttt ... caaactgcagTAATATATTTCGTGTTTTCGGTCGTCCTCCGGGAAGCATAGAGGCAACAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGTGATCTGTACGAGAATGACTCAATTTTCGACAAGTTTGAGTGCTGTCTTAGTGGGGATGGACTTCGTGTTGCAACTGGTTCTTATGGgtatttctttcatccattattgactgtacgtgtcattttaaagaaatcctctctattaacacttccattttctggtgtcttcaaactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA