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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag

Basic information

species Zea mays
transcript GRMZM2G109987_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g01890.1 (Oryza sativa), 5'ss of exon 2
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaag---tcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag--
||||||||| |||||| ||  |||||||||||||||| ||||| || |||||  | ||||||||||| ||||||||||||||||||||||||||| | ||||||  |        | | |||    || | ||     | | |      |||   | || | |   || || |  |  ||  || || || |   ||||    ||   
CCAAGCCAACCTCCTCCCGCAGGCAGCAACTGCTGCGTGAGTGCCCCATACTTGCTAACATTGAGCCCAAGCAGATCAAGGTCTGGTTCCAGAACAGAAGgtaatgataatag--aattgaatctttctacgtttgttctctgt--gacaaaaacttgttatggcagttttccctgattgt-ttcatctgtc---acctgaaataaca

upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA11G20520.1 (Glycine max), 5'ss of exon 1
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag
| ||||| || ||    ||| |||| ||| || |  | ||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||||||| |||| |  ||    |||| || ||  | |  |  || |    | | ||  ||| |  |  | |  |  | | |  | || |     |    || |   | || ||
CTAAGCCTAGTTCTCTGCGGAGGCAACAATTGATCAGAGAGTGCCCCATTCTCTCCAACATCGAGCCTAAGCAAATCAAGGTTTGGTTCCAGAACCGTAGgtgagtaac---acaaatc-aaccctattttaagtc---cctctcttcattctttttgaaattggttcttagatgtgaa-----ggttttggatggtgtgcag

upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA12G08080.1 (Glycine max), 5'ss of exon 1
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag
| ||||| || ||     |  |||| ||| || |  | ||||| || || ||||||||||| ||||| ||||| |||||||| |||||||||||||| |||| |    ||   ||| || |        |   |||    | |  |   |  |  |   ||| ||  |||     | |||    |    ||     | |||||
CTAAGCCTAGTTCTCTGAGAAGGCAACAATTGATCAGAGAGTGCCCCATTCTCTCCAACATCGAGCCTAAGCAAATCAAGGTTTGGTTCCAGAACCGCAGgtga---gtcactcaaatcaacactactttaaggcc---cctcgttctttcatgtttctgaaagtggttc----ttagatgtggggttttgggtggtgtgtag

upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G60690.1 (Arabidopsis thaliana), 5'ss of exon 1
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag--
| ||||| |||||    || || || ||| || | || || ||| | ||  |  |||| |||||||| ||||||||||| |||||||| |||||||| |||||     ||     | |    | |    |  |     |    |  |  ||| | |  |     | | |    | | |  |  | |          | || ||  
CTAAGCCTAGCTCTCTCCGTCGACAACAATTGATCCGTGAATGTTCCATTTTGGCCAATATTGAGCCTAAGCAGATCAAAGTCTGGTTTCAGAACCGCAGgtattgcttctctttaat-atggccaggattaatttttaattaaggattttgaatttgat----tctattggatttagtgtgttatattcaatggatatgaagga

upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv06s0004g02800.t01 (Vitis vinifera), 5'ss of exon 1
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag-----
| ||||| || ||    ||||||||||| ||| | || ||||||||||| ||||| || |||||||| ||||| ||||| |||||||| ||||| || ||||   ||||   | || ||||        ||| |   ||   |     ||| |  | |    ||   ||    |||  |||  | |  |  ||| |    ||      
CAAAGCCCAGTTCTCTTCGGCGGCAGCAGCTGATCCGGGAGTGTCCTATTCTCTCTAATATTGAGCCCAAGCAAATCAAAGTCTGGTTTCAGAATCGCAGgt--taaataaaataa-tcgatacta---tcgggtttcatttcctctgattttgttcatctgcggcattttgatct--atttctctcacaatacttcacttatgacaa

upper sequence: GRMZM2G109987_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv13s0019g04320.t01 (Vitis vinifera), 5'ss of exon 1
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaa--tccgacaagtcgaagtcga--agtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag
| ||||| |||||| | || |||||||| ||| | || ||||| || || || |||||||||||| ||||||||||||| |||||||| |||||||| |||| |      |  |    |     || ||  ||| | || |    |   | || | |  ||      ||  |||  |  || |  |      | |   | ||     
CGAAGCCCAGCTCCACTCGCCGGCAGCAGCTGATCCGGGAGTGCCCGATTCTTTCCAACATTGAGTCAAAGCAGATCAAAGTCTGGTTTCAGAACCGCAGgttagggggtttgggttgggaatggtggatcagttgtgctattttct--tgaaatttgttgtttgttgtgattc--gcttgcacgagaacaacggcttcctcac---

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|149099239|gb|EE185269.2|EE185269
EST:     CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAG                         GTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
genomic: CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatc ... ccttctgtagGTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
EST: gi|78083168|gb|DV511561.1|DV511561
EST:     CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAG                         GTGCCGCGATAAGCA
genomic: CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatc ... ccttctgtagGTGCCGCGATAAGCA
EST: gi|30087093|gb|CB885301.1|CB885301
EST:     CTCTCCAACATTGAGCCAAAGCAGAACCAGGTCTGGTTCCAGAACCGGAG                         GTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
genomic: CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatc ... ccttctgtagGTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
EST: gi|28873580|gb|CB329550.1|CB329550
EST:     CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGCTCCAGAACCGGAG                         GCGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
genomic: CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatc ... ccttctgtagGTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
EST: gi|149080026|gb|EE169046.2|EE169046
EST:     CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAG                         GTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG
genomic: CTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatc ... ccttctgtagGTGCCGCGATAAGCAGCGGAAGGAGTCTTCGCGGCTTCAGGCTGTGAACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGCCAAGCTCCTCACGGCGGCAGCAACTGCTGCGCGAGTGTCCTATACTCTCCAACATTGAGCCAAAGCAGATCAAGGTCTGGTTCCAGAACCGGAGgtaacaaatccgacaagtcgaagtcgaagtcgagccacagcccactaaattgtagtgaagaacgtatttcacgtctggattaatgtgcctgtaccttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA