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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagtacacctcatagtgtaggttaatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA

Basic information

species Zea mays
transcript GRMZM2G097502_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 2
-tagtacacctcatagtgtaggttaatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattg--aaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA
 |   | |  |  ||       ||| |  | | |  ||  |    ||| |||          ||||  |   | ||  ||     | ||   |||  |||||||||||||||||||||||  ||||||| || ||| |||||| ||| |||| ||| |||||||||||||||||||| ||||| ||||||||| |||||||||
atgacagattttttatctaccattattaatttttcaat--ctatcattcttaatggttttaatctagaaaaaa-atcagtcttaatgcttacttgctaaacagGTTTCAGAAGTGAGCTCCCTTTTAGGCAGGGCTGGCACTGTTGGTCTTGGAAAAGCAGTGGAGGTTCTAGATACGCTTGGTAGTAGCATGTCAAGTTTAA

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 4
-tagtacacctcatagtgtaggt---taatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA
 |    |  | |    |  ||||   ||| |||   | | |  |  | |     |   | ||   |  ||      | |||  |  | |  ||   |   |||||| ||||||||||| ||| |||| ||  ||||| | || ||||||||||  |||||||| || ||| | || ||||| |||||||| ||||||| ||| |
cttccccttccctatttccaggtctttaaggcttcctatgtaactaaaaaa---aaaaaagcgattagattgccttt-ttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA

upper sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 1
---tagtacacctcatagtgtaggttaatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA
    | |     ||||  | ||  ||  |  |||| |  ||       ||  | | |    || | ||  |  ||  ||  |   ||   | |  |  | ||||||||||||||||||||| |||| || || ||| | |||||||||||||  |||||||| || ||| | || |||||||| ||||||||||||| |||  
acagaatgatattcattat-tatattggtaatgtgatgttgaattgtcttaatggatcaatatttttagtag-cactttaatggattgatt-tggtataccagGTTTCAGAAGTGAGCTCACTTTTGGGCAGGGCTGGTACTGCTGGGCTTGGGAAGGCAGTTGAAGTTTTGGACACACTTGGTAGTAGCATGACAAATTTGC

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|211033161|gb|FL324562.1|FL324562
EST:     GCTGGTGTGGGCAAGGCAAAAGCCGGCGCTGCCAAG                         GTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAA
genomic: GCTGGTGTGGGCAAGGCAAAAGCCGGCGCTGCCAAGgtttgaggaa ... attgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAA
EST: gi|149013699|gb|EE043151.2|EE043151
EST:     CGCTGTCCCAGAGGGCTGGTGTGGGCAAGGCAAAAGCCGGCGCTGCCAAG                         GTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAA
genomic: CGCTGTCCCAGAGGGCTGGTGTGGGCAAGGCAAAAGCCGGCGCTGCCAAGgtttgaggaa ... attgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA
                                 ttcctttcctgtatt  CT-rich tract
                      attcatatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagtacacctcatagtgtaggttaatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG