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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGTGAAGATTGCAGAGCATAAGCTTACTGGACATAGGGTTGCTATAAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttgttatccagtcattttgcattttcactaatatttttttgataataaacaagtttagttttaatagtgcttttgataatattaatacatggagttgctttgataattaagaccacatccctccctatcatgtttccag

Basic information

species Zea mays
transcript GRMZM2G107867_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 5'ss of exon 2
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACTGGACATAGGGTTGCTATAAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttgttatccagtcattttgcattttcactaatat----ttttttgataataaacaagtttagttttaatagtgcttttgataatattaatacatggagttgctttgataattaagaccacatccctccctatcatgtttccag
|||||||||||||||||||||||||||||||| ||||| || ||||||||||||||| | ||| |||||||||||||||||||||||||||| ||||||||||    |  || || |   |     |||||| |  ||| |    | || ||     | |  |  |||  ||   |  | | | |  |  |  | ||   || |                                              
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGACACAGAGTTGCTATAAAGATCCTGAACCGCCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgta-acctccttttctaaagagac--cattttaatcaatctattatcttctgtgctcatatgatcttaagttacttgcttcctgtagtggt-ctgatctgtgaa----------------------------------------------

upper sequence: GRMZM2G107867_T04 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 5'ss of exon 2
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACTGGACATAGGGTTGCTATAAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtt-tgttatccagtcattttgcattttcactaatatttttttgataataaacaagtttagttttaatagtgcttttgataata--ttaatacatggagttgctttgataattaagaccacatccctccctatcatgtttccag
|||||||||||||||||||||||||||||||| || || || ||||||||||||||| | ||| | |||||||||||||||||||||||||| ||||||||||   |  | ||||  ||  |     || ||| |  ||| | || |      |   || | | |  | | |   |||||   ||| |    | |||  || | |                                            
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACAGGGCACAGAGTTGCTATAAAGATCCTGAACCGTCGCCAAATGAGAAATATGGAAATGGAGGAGAAAGgtaccttccttttataaagagac----cactttaatcaatctattatcttctgtgttcatgatcatatgttacc-tgcttcctatagtggtctgatatgtgaact--------------------------------------------
















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|148999574|gb|EE036551.2|EE036551
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|60359581|gb|DN226554.1|DN226554
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|71329108|gb|DR801263.1|DR801263
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|89758870|gb|DY687889.1|DY687889
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|71447675|gb|DR828725.1|DR828725
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|211440534|gb|FL230371.1|FL230371
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|71437399|gb|DR818449.1|DR818449
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
EST: gi|211427353|gb|FL101766.1|FL101766
EST:     AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAG                         CAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC
genomic: AAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttg ... atgtttccagCAAAGAGAGAATTCAAGATATTGAAGTTGTTCATTCACCCCCATATCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAAGTGAAGATTGCAGAGCATAAGCTTACTGGACATAGGGTTGCTATAAAGATCATCAACTGCCGCCAAATGAGAAATATGGAAATGGAAGAGAAAGgtatggtttgttatccagtcattttgcattttcactaatatttttttgataataaacaagtttagttttaatagtgcttttgataatattaatacatggagttgctttgataattaagaccacatccctccctatcatgtttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA