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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag

Basic information

species Zea mays
transcript GRMZM2G095348_T03
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 5'ss of exon 21
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccatt-agaaaaaaatgcatgctattatcttattctttttt-----tctgtaccttgtatgcag
 |  |||||||||||||||||  ||||||| || || |||||||| ||||||||  | || ||||||||||| |||||||| ||||||||||||||||||||||||| ||||  ||||| ||||     ||||||||||| | ||||  |||||| | |   || |||| |  |  | || | |     | ||| |||| | | |||
CAATCGTATACCTGAAGCTGCGTTAATGGCACGTTCTTATCTTCCCAGCAAAGTTTCTGAGATAGTAGCAATATGGAGAAATGACCTCAGTAAAgtaatttcttaatcttctgctctta-tctttgcattgaaaagtgtgcttccatccagaaaacattttctgttattgttctggttttatctattcatatgttccttctgtacag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 21
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag
 |  || || || || || ||  ||||||| ||||| ||||| || || || ||  |||| ||||| |||||||||||||| ||||||| ||| ||||||||| | |    |        | | |||       |   |  ||   ||  |      |||||| |||||| |||| |   |   ||| |   | ||     
CAATCGAATTCCGGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctgattcaggtagatggtatttacttatgtttgaacttcctgtt-ttttacctttgtgcatgatattatattatgcgaat---ctgaattctctaca---

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 10
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtg-gtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag
 |  || || || || |||||  ||||||| ||||| ||||| || ||||| ||  |||| ||||| |||||||||||||| || |||||||| ||||||| |||   |||| || |   | |   |    | |  |         |||    ||      |  ||   || |   |  |        ||| |||       
CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatttgtta---ttctgatatatatatgtatatatatacatacatacataatttagtaatggaatagcctgacatttatgtggtgcacatgatactttggg-----

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 21
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttctta-----atgttctcatcttagtcttctttctgaaaagtgtgg--tgccattagaaaaaaatgcatgctattat---cttattctttttttctgtaccttgtatgcag-----------------------------------------------------------------------------------
 |  || || || || |||||  ||||||| ||||| ||||| || ||||| ||  |||| ||||| |||||||||||||| || |||||||| ||||| |  ||     || |    || |   | |  |||   ||  |  | |  || ||||           |||| || | |         ||| | ||||    |   |   | |                                                                                   
CAATCGGATTCCAGAGGCTGCTTTAATGGCTCGATCCTATCTCCCAAGCAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGATCTCAGTAAGgtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: GLYMA13G43680.1 (Glycine max), 5'ss of exon 21
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag
 |  || || || || || ||  ||||||| ||||| ||||| || || || ||  |||| ||||| |||||||||||||| ||||||| ||| ||||||||| | |    |        | | |||       |   |  ||   ||  |      |||||| |||||| | ||     |   ||| | | |  |     
CAATCGAATTCCAGAGGCAGCTTTAATGGCTCGATCTTATCTCCCAAGTAAGGTCTCAGAGATAGTGGCAATTTGGAGAAAAGACCTCAATAAGgtaatttctgattcaggtagatggtatttacttatgtttgaacttcctgtt-ttttacctttgtgcatgatattatataatgggaat---ctgaatcctccaca---

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 25
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag
||  || ||||||||||| || || |||||| ||||||| ||||| ||||| ||  | |||||||| ||| | |||||||||||  | |  || || | |  |  |      |     |  ||| |   ||||              |    | | || ||   | ||   | || || | |      |   || ||  ||
TAATCGAATACCTGAAGCCGCTCTGATGGCGAGATCGTACCTTCCAAGCAAGGTCTCCGAAATAGTGGCATTGTGGAGAAACGATTTGACCAAGgttagtggtagacacatccgatgca-ccttgtgattgaatttcaaaccttgcctgttgagatatccacaatttttcttcatcctctgtc-----aatctggatatag

upper sequence: GRMZM2G095348_T02 (Zea mays), 5'ss of exon 20
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 21
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag
||  || ||||||||||||||  ||||||| ||||| || ||||| ||||| || ||||| ||| |  | ||||||||||| |||||||  || || |||  |     |  | || | | | |  ||||    |||     ||   |||| |||  ||    |  ||      |             |      | ||   
TAATCGGATACCTGAAGCTGCTTTAATGGCACGATCTTACCTTCCAAGCAAGGTTCCAGAGATAATCACGATTTGGAGAAATGACCTCAACAAGgttattcttc----tgattatttcattttgttttccatgaagcactttg--gttagtaaatcatatccgagatagagagaggacaacaaatgatgatgaatgtgat-

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|32934072|gb|CF038884.1|CF038884
EST:     GTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAA                         ATTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAATATCCAAAT
genomic: GTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttctt ... ttgtatgcagATTAATCCAAAAGCTGCAGAGTCTCTGGCAGATCCTTCTGAATATCCAAAT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCCGTATACCTGAAGCTGCACTAATGGCGCGATCGTATCTTCCTAGCAAAGTACCAGAAATAGTAGCAATTTGGAGAAACGACCTCAGTAAAgtaatttcttaatgttctcatcttagtcttctttctgaaaagtgtggtgccattagaaaaaaatgcatgctattatcttattctttttttctgtaccttgtatgcag

- - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA