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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG

Basic information

species Zea mays
transcript GRMZM2G079538_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 9
acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgat----ttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   || |   ||   |   |   | | | | |   |     ||| |||    | | |  ||| ||  | || || |  || | | | |      ||  ||||||||| |||||||||||||| || ||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||||
---tagaatcttgcatggcgtactactaattcttcctagaaaagcttggctagatatgcttttct-gttttgtccccttaccctgttaagacaatacaatgcagGACTAATTTGATGAAGCTGCGGTCTGATTATAAGGATGAGTTTGTCACCAAGCACGGTGTCAAATTGGGTCTGATGTCCTGCTTTGTCAAG

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA02G46200.1 (Glycine max), 3'ss of exon 11
------acttaaataattatct--tttgccatgccattacg-atcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
         |   |  || |    |   | |  |  ||| | || |  | ||  |     |  |||||| ||     ||||| ||| |    |     | || ||  ||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| || |||||||| ||||||||| |||||||||| 
agatttttcttggtctttgtgagatcaacaaacctgttatgcattctctcaaattcactattatgtattctctcc--cttattgctctgctct-----taatgat--agGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTCAAA

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA14G02530.2 (Glycine max), 3'ss of exon 11
-acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
   |||| |    ||  ||     ||   || |  ||   |     |  ||||||  || | |  | ||  | |  ||   |  | || | |       ||||| |||||||||||||| |||||||||||||| ||||  |||||   ||||||||| || |||||||| ||||||||| ||||||| || 
tgtttaattgccaattcttgatgttgtgtttcctgtcatgtccttat-atagtggattactattgtcattctcttccttattggtctgctcttaatgatagGACTAATTTGATGAAGCTCCGTTCTGATTATAAGGATGCTTTTGTTGAAAAGCATGGAGTCAAATTGGGGCTTATGTCTGGCTTTGTGAAA

upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 9
lower sequence: Vv19s0090g00750.t01 (Vitis vinifera), 3'ss of exon 6
----acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
       || ||| | |  ||     | ||  ||  |    ||   |||   |  |||||  ||||   | | || | |||||  |||     ||||  ||||||||||||||||||||||||||||||||||||||||||| |||| |   |||||||||||| || ||  |  |||||||  | ||||| |||
tcatcaatatatattgaaattgcctgacgcattttagcatgctatcaggcacttctggtgatttttgtctgtttt-ttgctgtg-cttgctgcttat--tgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGCATTTTTTGAAAAGCATGGTGTGAAGTTAAGATTTATGTCAGGGTTTGTTAAG

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|211104575|gb|FL031921.1|FL031921
EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|148950981|gb|EC896624.2|EC896624
EST:     ATTCTCAGAACACCTTTGCAATGCTGAGTACATTTTAATGAAGT-GACAT                         GACCAATTTGATGAAGCTTCGTTCTGATAA-AAAGATGAATTTGTCACAAA
genomic: ATTCTCAGAACACCTTTGCAATGCTGAGTACATTT-AATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|211169880|gb|FL077609.1|FL077609
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|32830086|gb|CD969764.1|CD969764
EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|31355590|gb|CD439947.1|CD439947
EST:     GATTCTCAGAACACCTTTGCTATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTTGATGA-GCTTCGTTCTGATTATAAAGA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTT-GATGAAGCTTCGTTCTGATTATAAAGA
EST: gi|13558100|gb|BG549456.1|BG549456
EST:     ATTCTCAGAACACCTTTGCAATGTTGTGTTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ATTCTCAGAACACCTTTGCAATGCTGAG-TACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|32942914|gb|CF047733.1|CF047733
EST:     GAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|60358853|gb|DN225826.1|DN225826
EST:     GTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|6227238|gb|AW155837.1|AW155837
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|32829046|gb|CD968724.1|CD968724
EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|32828877|gb|CD968555.1|CD968555
EST:     ACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: ACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|211169873|gb|FL077602.1|FL077602
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|7145229|gb|AW506710.1|AW506710
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|13558537|gb|BG549893.1|BG549893
EST:     ATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGTTGTTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAA
genomic: ATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAG-TTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAA
EST: gi|32867030|gb|CF006712.1|CF006712
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
EST: gi|67019048|gb|CO447797.1|CO447797
EST:     GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACAT                         GACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA
genomic: GATTCTCAGAACACCTTTGCAATGCTGAGTACATTTAATGAAGTTGACATgtaagtgttc ... tattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG
                                 tatcttatgatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttaaataattatcttttgccatgccattacgatcccttgaaggttgtagtggtgtattttccttatcttatcgctgtatcttatgatttattatgcagGACCAATTTGATGAAGCTTCGTTCTGATTATAAAGATGAATTTGTCACAAAGCATGGTGTAAAATTGGGTCTTATGTCTTGCTTTGTCAAG

- - - - - - - - - - ccatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatc