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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaacttccaattgctaatcttgtatccttgtaacattggttcatacgatatcagttgacacatttttctcattttctgtcgtacttttcattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG

Basic information

species Zea mays
transcript GRMZM2G085438_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085438_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g49380.1 (Oryza sativa), 3'ss of exon 1
ccaaacttccaattgctaatcttgtatccttgtaacattggttcatacgatatcagttgacacatttttctcat--tttctgtcgtacttttcattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
| |    |  |||   |  |  |||   |  ||||  ||| |   | ||||  | ||||       ||||| ||  ||| | || || || ||||| |||||||||||| ||| | ||||||||||||||||
ctatgtctataatcaatggt--tgttatccagtaatgttgttgtgtgcgatgccggttggtcttgctttctaatcatttatctcttatttctcattctgtagATGGCTCCCAAGGGAATCCAGATGGAAGAG
















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|93016345|gb|EB641865.1|EB641865
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|71307182|gb|DR789758.1|DR789758
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|149076326|gb|EE164940.2|EE164940
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|78123599|gb|DV541983.1|DV541983
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|78106711|gb|DV525129.1|DV525129
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|71439067|gb|DR820117.1|DR820117
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|211083467|gb|FK983603.1|FK983603
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|78082086|gb|DV510498.1|DV510498
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|211083466|gb|FK983602.1|FK983602
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATG
EST: gi|78076593|gb|DV505027.1|DV505027
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|93015877|gb|EB641397.1|EB641397
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|37420223|gb|CF647800.1|CF647800
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|71439017|gb|DR820067.1|DR820067
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|71426297|gb|DR807347.1|DR807347
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|50333020|gb|CO528146.1|CO528146
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|148973073|gb|EE024135.2|EE024135
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
EST: gi|50329341|gb|CO524467.1|CO524467
EST:     GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAG                         ATGGCTCACAATGAAATCCAGATGGAAGAG
genomic: GGGCCGCCTTCGCGCCCGTGCTCCCCACCCTCGACCACTGCCTTTTCAAGgttcgatgtg ... cattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgatatcagttgacacatttttctcattttctgtcgtacttttcattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG
         agttgac  putative branch site (score: 4)
                   tttttctcattttctg  putative PPT
                  atttttctcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaacttccaattgctaatcttgtatccttgtaacattggttcatacgatatcagttgacacatttttctcattttctgtcgtacttttcattttgtagATGGCTCACAATGAAATCCAGATGGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA