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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatttaatcagtttttatgctttagttttatagtttagttcctcttgctgagacaggcggactagaaatccaaatttgctgatgctctcatttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG

Basic information

species Zea mays
transcript GRMZM2G180815_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180815_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g44394.1 (Oryza sativa), 3'ss of exon 9
aaatttaatcagtttttatgctttagttttatagtttagttcctcttgctgagacaggcggactagaaatccaaatttgctgatgctctcatttgt-ttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG
 | ||   ||     | |    | | |  | | || |  |||   ||| |  || |        |      ||       ||     || |  ||| ||||||||| |||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||| ||||| |||||||  |||
-atttggctcgaacatcaactataaatgattttgtattcttcagattgttctgaaatttaattaaattgctcacgcaacttgtcttgctgacctgtgttagGTATGCTATGATTGGAGCAAGGGTGCCGAGAAGCACAATCCTTCTACTGCAAAAACAAATATCTTTCTCCATAGTGTCCAG

upper sequence: GRMZM2G180815_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA01G09290.1 (Glycine max), 3'ss of exon 9
aaatttaatcagtttttatgctttagttttatagtttagttcctcttgc-tgagacaggcggactagaaatccaaatttgctgatgctctcatttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG
    ||||  | | | ||   ||   || | |  | | |   |  |  | |||  |   | |  ||   ||     | ||         |||||| | ||||| ||||||||||||||||||||||| || || || |||||  |||| |||||||   | |||| | | ||     |||||
-tgcttaaaaaatatgtaaagttagtttgttttttgtggacacattgacgtgaccctttctgtttaattatttggctctgaaaccttgttcatttctgtagGTTTGTTATGATTGGAGCAAAGGTGCAGAAAATCACAATCCAGCTACAGCAAAGAACTACATATATTTGCACTTACCACAG

upper sequence: GRMZM2G180815_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA02G13780.1 (Glycine max), 3'ss of exon 9
aaatttaatcagtttttatgctttagttttatagtttagttcctcttgctgagacagg--cggactagaaatccaaatttgctgatgctctcatttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG
   || ||  | |   ||   ||   || | |  ||     | | |||  | |||     | |  ||   ||     | ||         |||||| | ||||| ||||||||||||||||||||||| || || || |||||  |||| |||||||   | |||| | | ||     |||||
--cttaaaaaaatacgtaaagttagcttgtttttttgtaggcatattgacgtgaccctttctgtttaattatttggttctgaaaccttattcatttctgtagGTTTGTTATGATTGGAGCAAAGGTGCAGAAAATCACAATCCAGCTACAGCAAAGAACTACATATATTTGCACTTACCACAG

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|60352181|gb|DN219154.1|DN219154
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|71758033|gb|DR955970.1|DR955970
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTTTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|211532431|gb|FL471823.1|FL471823
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|9254555|gb|BE345023.1|BE345023
EST:     CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CCATCACATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
EST: gi|74235194|gb|DT643108.1|DT643108
EST:     CATCACAATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCG                         GTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA
genomic: CATCAC-ATGCAGCGCATTCAATCATGATGGCTCTATATTTGCTTACGCGgtaggtcatt ... atttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctgagacaggcggactagaaatccaaatttgctgatgctctcatttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG
                                tgctgat  putative branch site (score: 3)
                                        ctctcattt  CT-rich tract
                                             atttgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatttaatcagtttttatgctttagttttatagtttagttcctcttgctgagacaggcggactagaaatccaaatttgctgatgctctcatttgtttagGTATGTTATGATTGGAGCAAAGGTGCTGAGAAGCATAATCCTTCTACTGCAAAGACAAATATATTTCTACATAGTGCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG