Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatgggactattgaacctgtggaggaagtaatttgatttcagtcatatccttttcatgataataataactaactcggcctcttctcgcttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG

Basic information

species Zea mays
transcript GRMZM5G800112_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G800112_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g27850.2 (Oryza sativa), 3'ss of exon 2
atgatgggactattgaacctgtggaggaagtaatttgatttcagtcatatccttttcatgat----aataataactaa-ctcggcctcttctcgcttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG
                                                   |||||||| ||    | |  |  |||| | |    | |||||     |||||||||||||| ||  ||||||| |||||||| || ||||||||||||||||| || |||||| |||| |||||||| ||||| |||
---------------------------------------------------cttttcattatttctactgttctctaatcccttgttattctcaacatatgctagatgagcgtgtctcaagtgacctgaagaaaaacctcatgcaagcaagGCTGGACAAGAAGATGACCCAGGCACAGCTTGCACAG

upper sequence: GRMZM5G800112_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os08g27850.1 (Oryza sativa), 3'ss of exon 2
atgatgggactattgaacctgtggaggaagtaatttgatttcagtca--tatccttttcatgat----aataataactaactcggcctc-ttctcgcttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG
       | |    |||    |  |   | |   ||  ||  | |    | |||||||||| ||    | |  |  ||||  |    |  |||||     |||||||||||||| ||  ||||||| |||||||| || ||||||||||||||||| || |||||| |||| |||||||| ||||| |||
-------gccccgagaaagcataaattcaatctattacttggacttgcttgtccttttcattatttctactgttctctaatcccttgttattctcaacatatgctagATGAGCGTGTCTCAAGTGACCTGAAGAAAAACCTCATGCAAGCAAGGCTGGACAAGAAGATGACCCAGGCACAGCTTGCACAG
















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|211137933|gb|FL090170.1|FL090170
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|211137002|gb|FL090161.1|FL090161
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|211137930|gb|FL090167.1|FL090167
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCA
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCA
EST: gi|211137007|gb|FL090166.1|FL090166
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGGCT
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTT-CCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGG-CT
EST: gi|101399867|gb|EB821780.1|EB821780
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|211142486|gb|FL118083.1|FL118083
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|211136052|gb|FL090147.1|FL090147
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|15208834|gb|BI430718.1|BI430718
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCC                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCG
EST: gi|211137931|gb|FL090168.1|FL090168
EST:     TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCC-                         ATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCA
genomic: TACATCCCTCAACACCAAGCGCCTCGACGACGACACCGAAAACCTCGCCCgtgagcaatc ... ttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatccttttcatgataataataactaactcggcctcttctcgcttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG
                                  cctcttctcgctt  CT-rich tract
       ttttcatgataataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatgggactattgaacctgtggaggaagtaatttgatttcagtcatatccttttcatgataataataactaactcggcctcttctcgcttaatgctagATGAGCGAGTTCCAAGTGATCTGAAGAAGAATCTCATGCAAGCAAGGCTCGATAAGAAGCTGACACAGGCACAACTTGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
-tgatggg
- - - - - - - gaacctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tttcatg