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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag

Basic information

species Zea mays
transcript GRMZM2G421857_T03
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctt--taaact---ttgcctaatgttatctgcag
|||||| |||||| | |||||||| ||||| ||||| || ||||| ||||| ||||| ||||| ||||| || ||||||||||||||||||||||||||||||||      |   |  || ||  |     |      ||| | | | || |||    | | | ||  ||| |||||| | ||| |  |  | |  |   | ||||       |||||||
TGTACTTGATGCATTGTTCCCCTCAGTTCTTGGAGGAACATGTGCCATTCCTGGAGCTTTTGGTTGTGGAAAGACTGTCATTAGTCAGGCACTTTCCAAGgtgatcactatttttctattcctcattgccatgtagtatctatagaaactatac----tctctttttgttgccttgatcacatctttgtactgagatgaatagcctctcaaactctgcag

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
||| || ||||| || |||||||| ||||| || || |||||||| || || ||||| ||||| |||||||||||||||||||||||||| ||||| |||||||  ||     ||||| |   |    || |        ||  |    | | | || ||  ||||  |  ||          | | |||   |                     
TGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTAAGgtgaacttaatataccctattaaaacaataattttttaattgaagatattctccgtaattcatctttttcctccacccacccccctgttttggcag-------------------

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
||| || ||||| || |||||||| ||||| || || |||||||| ||||| || || ||||| ||||||||||| |||||||||||||| ||||| |||||||  ||    ||||||  | ||   | | |     ||   |||||| | | |   |  ||  |||||  | ||      | ||  |  |                        
TGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTAAGgtgaacttaaaacaccct--aataagacaa-tgattttttaattgtagatattc---tccttaattcatctttttcccccaaccacttgcag-----------------------

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
||| || ||||| || ||||| || ||||| || || || ||||| ||||| || || ||||||||||| |||||||| || |||||||||||||||||||| |  ||    ||| ||   ||  |  |  |||      | |  |  ||| | | |||   | | ||  |   | |   | || | |||| |                      
TGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCAAGgt-accttgtgacactct---ctggttttgttcca-----tttaattactggatagattgaatttccaaagc--taactttttcttatttacatag-------------------

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
||| || ||||| || || ||||| || ||||| || |||||||| ||||| || |||||||||||||| ||||| ||||| ||||| || ||||||||||||  |||| |      |||||||      ||     || |  | | | || | ||| || ||||   |     | |||  || | | | ||  | | |      | || |||||
TGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCAAGgtgtatttctcat-ttgtttactag----gcttttgtttttaatat-gttggaaataattcttctatctcagtctcatg-cattagcat-aacatctac------tcatttgcag

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag-------------------------------------------------------
| |||||||||| |||||||| || ||||| ||||| ||||| || ||||| || |||||||| ||||| || |||||||||||||| || || || |||||  ||        |  |||     |         | ||  |         ||||| |||| | ||  || ||||  || |    | ||||| ||      | | || | || ||                                                       
TATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTAAGgtagttggttacatctgtttggatttttcgaagttcatttcgc----atcatacattttttctttttcttttctt--tggttgtgtatttaagctgcagaaactattgtttgaagtttgtatgaaagttctggaacgaggcttattttttgcaaatttgtttgtgtgcag

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
  |  ||||||| || || || || || ||||| || || ||||||||||| ||||||||||||||||| || || || ||||||||||| ||||| |||||  ||     ||    |||   |  | |      | || |  || | | |                                                                
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttc---ttttgtaatgcgtgactaactttgtcatgaaacag----------------------------------------------------------------

upper sequence: GRMZM2G421857_T03 (Zea mays), 5'ss of exon 10
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 9
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag
  |  ||||||| || || || || || || || || || ||||||||||| ||||||||||||||||| || || || ||||||||||| ||||| |||||  ||     |||   |||   |  | |      | || |  || | | |                                                                
CATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttggagttca---tttgtaatgcgtgactgactttgtcatgaaacag----------------------------------------------------------------

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|6012344|gb|AW061700.1|AW061700
EST:     CAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCCCTTTCCAAG                         TACTCCAATTCCGAAACTGTGGTTTATGTGGGCTGTGGTGAACGAGGAAAC
genomic: CAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttcc ... ttatctgcagTACTCCAATTCCGAAGCTGTGGTTTATGTGGGCTGTGGTGAACGAGGAAAC
EST: gi|6636981|gb|AW261253.1|AW261253
EST:     CAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAG                         TACTCCAATTCCGAAGCT
genomic: CAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttcc ... ttatctgcagTACTCCAATTCCGAAGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACTGGATGCACTATTCCCCTCGGTTCTGGGAGGCACTTGTGCTATTCCAGGAGCATTTGGCTGTGGTAAAACTGTCATTAGTCAGGCACTTTCCAAGgtgattttccctcaccctttactactcctactcccccttctgttgtagctgtacatattttttcttcattgtcttgatgatatcatctttaaactttgcctaatgttatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA