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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgccttgaagtttgaaccattcactgatttttgaactatctcactgatctccccctcccccatgcgtacattgaaatactcattggcttgcagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTGTTATTGAGCTTTCTCAAAATATTATCCAG

Basic information

species Zea mays
transcript GRMZM2G007871_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007871_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g24180.1 (Oryza sativa), 3'ss of exon 8
-----tgccttgaagtttgaaccattcactgatttttgaactatctcactg--atctccccctcccccatgcg-tacat--tgaaatactcattggcttgcagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTGTTATTGAGCTTTCTCAAAATATTATCCAG
     |   ||| | ||       ||   | |  | ||||    |   |||   ||| |   |    | ||   |||||  | | ||  |  ||||||||||||||||| |  ||||||||| |||||||||||||||||||||| |||||||| || |||| ||||||||||| |||||||| ||||||
aaacttatgttggaattca---tttttgtttacatgtgaatgggcatgctgctgtctgcatttgtttcttgttctacattctaatatgtttgttggcttgcagATTGCACTACTACCAAGGAGTCCCCATGGTTTTGGATGGCTCAGGCCTGCAATCGGTGTAATTGAGCTTTCCCAAAATATCATCCAG
















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|32838158|gb|CD977836.1|CD977836
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|22935564|gb|BU571839.1|BU571839
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGG
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|26560014|gb|CA832249.1|CA832249
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGN
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|32837602|gb|CD977280.1|CD977280
EST:     ACATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGNTACNG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTG
genomic: ACATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTACTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTG
EST: gi|87156492|gb|DY401281.1|DY401281
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|32836675|gb|CD976353.1|CD976353
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|87157186|gb|DY401975.1|DY401975
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
EST: gi|87157024|gb|DY401813.1|DY401813
EST:     CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGATTGCAG                         TTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT
genomic: CATGCTTGAACTTGCACCTCGTCTTCTGGAAGAACTCGTTAAGGTA-CTTgtttgaatgt ... cagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctccccctcccccatgcgtacattgaaatactcattggcttgcagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTGTTATTGAGCTTTCTCAAAATATTATCCAG
 cactgat  putative branch site (score: 3)
                        attgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgccttgaagtttgaaccattcactgatttttgaactatctcactgatctccccctcccccatgcgtacattgaaatactcattggcttgcagattgcagTTTTACCAAGGAATCCCCATGGTTTTGGATGGCTCCGGCCTGCACTCAGTGTTATTGAGCTTTCTCAAAATATTATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
tgccttg
- - - - - - - - -cattcac