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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttttgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag

Basic information

species Zea mays
transcript GRMZM2G124886_T02
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 15
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggt-tttttgtcac-ttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag
||||||||||||||||||  |||| ||||| ||||||||||||||||||||||||||||||||||||||||  || ||||||||||| ||||||||||||||  || ||||  | |  | |||||  ||| | | ||||  ||   ||||||   || | |   ||||        |   ||||| |||  |||| ||||||
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTCACGACTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatgcat-tcacatatgatttg-gttagactgttaattttcagag-------gtagtataactattcgatgtattacag

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 5'ss of exon 6
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggt-tttttgtcac-ttaaaaagacatc-ttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag
||||||||||||||||||  |||| ||||| ||||||||||| ||||||||||||||||||||||||||||  |||||||||||||| ||||||||||||||  || ||||  | |  | ||||| ||||  | | ||||  ||   |||||| | || | |   || |        |   ||||| |||  |||| ||||||
TCATGAGATCAATGAACGCATCCGAACTGGCCTATGGGTTGGTGATTGTTTTATCTACAACAATTCTTCGTCACGGCTTAATTACTGTGTAGGAGGAGAGgtaagtattttcattatatcaaaaatacattgtcacatatgatttg-gttagacccttaattttcaggg-------gtagtataactattcgatgtattacag

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtg--ggttttttgtc--------------acttaaaaagacatcttatatatctttcaagttagatcatttag-tgatagagcgctttcatgtcataaccatttcatgtgttacag
 ||||| || |||||||||||| | || ||  | |||||||| ||||| ||||||||||||||||| || ||| | ||||||||||| || || || |||||      | |||  |                |||||||   ||  |  ||   |||  | ||  |  |    | | ||    |   || ||| |||||  |||     | |     
ACATGAAATGAATGAACGTGTCAGAACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATTCCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaagaattgtgcattcttttttaattgaactacaaggatcatgagacatcttgatg-cataatgattatgaatttag---

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtg---ggttttttgtcacttaaa----aagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtc-ataaccatttcatgtgttacag--------------------------------------------------------
|||||| || |||||||||||| |||| ||| | |||||||| |||||||||||||||||||||||||| ||| ||||||| || || || || || |||||      | ||||  |  ||| |    ||        |||| | |||    ||  |   |||  |   |       ||  |||  || |   | | || ||| | |                                                         
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAACAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttactcttttcccttttagattctaaagagctccatatttattt---attgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgt-atatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttag

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 4
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggt---tttttgtcactta-----aaaagacatct-tatatatctttcaagtta-----gatcatttagtgatagagcgctttcatgtc----ataaccatttcatgtgttacag------------------------------------------
|||||| || |||||||||||| |||| ||| | |||||||| |||||||||||||||| ||||||||| ||| ||||||| || || || || || |||||   |    ||||  |  |||     ||||||  ||| ||| ||| | |  |  |       ||||| |  |  | |    | |  || ||    ||    ||||  ||   ||||                                           
TCATGAAATGAATGAACGTGTCAGGACAGGGATCTGGGTTGGGGATTGTTTTATCTACAGCAATTCTTCTTGGAGGCTTAACTATTGTGTTGGTGGTGAGgtatttatacttttcccttttagattcaaaagagctctgtatttatttattgaactctcggtaatcatcttttctttgtcttcatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgttgcattacattatggatttag

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 15
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtg--ggttttttgtc-------------acttaaaaagacatcttatatat-ctttcaagttagatcatttag-tgatagagcgctttcatgtcataaccatttcatgtgttacag
 ||||| || |||||||||||| |||| ||  | |||||||| ||||| ||||||||||||||| | || ||| | ||||||||||| || || || |||||      | |||  |             | || |||| |    || |  || ||||  | ||  |  |    | | ||    |   || ||  |||||  |||     | |     
ACATGAAATGAATGAACGTGTCAGGACAGGCATCTGGGTTGGGGATTGCTTTATCTACAACAATACCTCTTGGAGACTTAATTACTGTGTTGGTGGTGAGgtattaactcttttcccttctagatttctagtttaaaaaaagaattgtgcattctttttaattgaactacgaggatcatgagacatcttgata-cataatgattatgaatttag---

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 19
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtggg-----ttttttgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag
  |||| | |||||||||||| ||||||||  |||||||||| |||||||||||||| | ||| ||||| ||| ||||||||||||| || || || |||||  |     ||| | |    ||  ||||| |  || ||| | ||| |  ||     | || | |||  ||  ||    |   || ||                 
CAATGAAACCAATGAACGTGTTCGGACTGGCTTATGGGTTGGGGATTGTTTTATCTATACCAACTCTTCTTGGAGGCTTAATTACTGTGTTGGTGGTGAGgtaaggctcatttctaggtttttggaaagaaacgttttatgttttttattttgttgtaatt-gagattcagtactcctcttatattacag---------------

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 15
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgg-gttttttgtca---cttaaaaagacatcttatatatcttt-caagttagatc-atttagtga------tagagcgctttcatgtcataaccatttcatgtgttacag
 |||||||  |||||| | ||  | |||||  |||||||||| || ||||| || |||||||| || || ||||||||||||||||| || || || |||||   || | |||||    |||     || |   | |  || | | ||  | | ||| ||||  ||       | ||||  |||  |   ||||||||      |||| |||
CCATGAGACAAATGAAAGAGTTAGAACTGGTATATGGGTTGGAGACTGTTTCATTTACAACAACTCCTCTTGGCGGCTTAATTACTGTGTTGGTGGCGAGgtattgtgtattgtccacccttgtcttgaaagtatttccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccat-----atgttccag

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: EFJ36319 (Selaginella moellendorffii), 5'ss of exon 10
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttttgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag
 ||||||||    || || ||  | |||||  ||||||| ||||||||||| || |||||||| || || ||| | || || |||||||| |||||||||||  | ||||          |  | | | |||||| | |||||   |   || |  ||                                          
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgctttt--------gtattgtcgt-ttatatttgtttcacacttcctcttccag------------------------------------------

upper sequence: GRMZM2G124886_T01 (Zea mays), 5'ss of exon 15
lower sequence: EFJ09529 (Selaginella moellendorffii), 5'ss of exon 10
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttt----tgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag
 ||||||||    || || ||  | |||||  ||||||| ||||||||||| || |||||||| || || ||| | || || |||||||| |||||||||||  | || |    ||||  ||| |      ||  | ||    ||| ||                                                       
GCATGAGATATCCGAGCGCGTGAGAACTGGCTTATGGGTAGGCGATTGTTTCATTTACAACAACTCGTCATGGAGACTGAACTACTGCGTTGGAGGAGAGgtctgcttctgtgttgtcgtttatatttgtttcacacatcctcttccag-------------------------------------------------------

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|60337834|gb|DN204807.1|DN204807
EST:     TTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAG                         GTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTT
genomic: TTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttt ... tgtgttacagGTTACAACCTTATTTCACTTGGATCGGCCAATGTATTTACTAGGATATCTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGAGATCAATGAACGTGTCCGGACTGGGCTATGGGTTGGCGATTGTTTTATCTACAACAATTCTTCGTGGCGGCTTAATTACTGCGTAGGAGGAGAGgtgggttttttgtcacttaaaaagacatcttatatatctttcaagttagatcatttagtgatagagcgctttcatgtcataaccatttcatgtgttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA