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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccaaatttctttttcatgctccctttgctctagttgtgctttctttaatggttctgttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG

Basic information

species Zea mays
transcript GRMZM2G009849_T02
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 27
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 44
gtatccaaatttctttttcatgctccctttgct--ctagttgtgctttctttaatggttctgttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG
|| |  |   ||| |||||||||||  |||  |  ||| |||| |||| | |||||||  |  ||  | |||||||||||||||||||||||||| || |||||||| |||||||||||||||||||| |||||||||||||||||||| |||||||||   ||||| || |
gtttgtat-cttcattttcatgctcagtttagttgctacttgttcttt-tctaatggtcatacttggagcagGATAATGCTGAGAGAACATCCTCATTCGTTGTGCTTATTAATTTGCTGAGGCCTTTAGACCCTTCAAGATGGCCATCCCCTACACCACCAGAGTCCCTCG
















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|194717113|gb|FK934266.1|FK934266
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGTTTAAAATCTTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|61118500|gb|DN559461.1|DN559461
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|87152573|gb|DY397362.1|DY397362
EST:     ATGGCAGCCAATTACTCAAAGCGCTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|32847226|gb|CD986907.1|CD986907
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
EST: gi|67035401|gb|CO463934.1|CO463934
EST:     ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTG                         GATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG
genomic: ATGGCAGCCAATTACTCAAAGCACTAAATGTTTTGATGCTTAAAATCCTGgtatccaaat ... ttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgctccctttgctctagttgtgctttctttaatggttctgttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG
                               ctttaat  putative branch site (score: 4)
                                        ttctgtttt  putative PPT
                            tttctttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccaaatttctttttcatgctccctttgctctagttgtgctttctttaatggttctgttttaaacagGATAATGCTGAGAGAACATCCTCGTTTGTTGTGCTGATTAATTTGCTGAGGCCTTTGGACCCTTCAAGATGGCCATCGCCTACACCAATGGAGTCTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG