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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG

Basic information

species Zea mays
transcript GRMZM2G018697_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 5
gatttttaataagaattaatgctt---gtatttgcgtct-caacatggaggcttcatgtgctcttgttc-tgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
   |  ||   ||  ||| ||| |    | |||  |  |    |    | | |  |||     |  |   |  ||   | ||  || | |||   |||||  |||||||| ||||||||||||||||| || ||||||||||| |||||||| |||||||||||||||||||||||||| || |||||||| |||||||||||||
---tcatatgcagtgttagtgcattcaatctttctgcttatggctcttaagttatatggaagttaatgaatataggaaaacttctcctgtcatttatgta--cagGATGTTACACTTCATGACCTTGACGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGGCAAATGATGAAGCCACGAAAGACTG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os07g08170.1 (Oryza sativa), 3'ss of exon 5
gatttttaata-agaattaatgc-ttgtatttgcg-tctcaacatggaggcttcatgtgctcttgttctga---agaggatctaatcttc--tcaccgatgt-atgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
         || || |||| ||  || |||    | ||||    |       ||| ||  | | | | | |   | ||     || ||||  | | | || |  | |||||||| || ||||||||||||||||| ||||||||||| |||||||| |||||||||||||||||||||||||| ||||||||||| ||||| || ||||
---------tacagcattagtgtgttatatacaggctctctgtttatgattctcaagttatatggatgttagttaaagagctgaaacttcagttatcaattttgtacagGATGTTACGCTTCATGACCTTGATGCTGCAAATGCTCAACCACAAGGAGGCCAAGATATTTTGTCCCTTATGGGACAGATGATGAAGCCACGGAAAACTG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 5
-----gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttg--ttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
     |  || || ||        ||   | || ||  |||  |||| ||   ||  | |  |  ||  |||| |    ||| |    |  |      |   |  ||||||| || || ||||| |||||||| || ||||| |  || ||||| || ||||||||| |||| |||||||| ||||||||||| ||  | || || |
tgagtggcttgtactagtgtactctgtaagaatgtgt-tctagacattgaatatt-gtatatttctgatttcttattgtgatttggattgtt-----gttcttaaagGATGTAACCCTACATGATCTTGATGCTGCCAATGCACGACCTCAAGGGGGACAAGATATTCTGTCTCTTATGGGTCAGATGATGAAGCCTAGGAAAACAG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------gatttttaataagaattaat--gcttgtatttgcgtctcaacatggaggcttcatgtgct--cttgtt-ctgaagaggatctaat-cttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
                                                           | | |  || | |||| |  |  ||| | |    || |      | | ||  |  |    |||||| || ||   || |  || ||| | || |||      ||||||||||||| || || || ||||||||||||||||  || ||||||||||| |||||  | ||  | |||||||| ||||||||||| || |||||||
gtttaccttctttgacctctcccttctgtgtagagtaattattttctttgttgatttattatctgttatgtattagtttgtatgtgtattaaccttagttcctaagtttattaagactacttgttactcaactagaccatatacttttgactgat------agGATGTCACACTCCAAGATCTGGATGCAGCAAATGCTCGACCTCAAGGTGGCCAGGATATACTTTCTTTGATGGGCCAAATGATGAAACCGCGGAAGACTG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 5
--gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
   |  ||  ||    || |    | || |  | | | ||   |||   |  |||||    |  |  |        |    | ||||   |  ||||  |||||||| |||||||||||||| ||||| |||||||| | ||| |||||||| |||||||| |||||||| ||||| ||||||||||| ||  | || || |
ctaaagttacatctttataaggtgtggtttcagagacaca--gtgggttccccatgttaattattcatcttctcattgcttttttcttttctctgtaatcagGATGTAACACTTCATGACCTGGATGCTGCAAATGCACGGCCTCAAGGTGGACAAGATATATTGTCCCTAATGGGTCAGATGATGAAGCCCAGGAAAACAG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------gattttta-ataagaattaatgcttgtat-ttgcgtctcaacatgg-aggcttcatgtgctcttgttctgaag----aggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
           |||| |||     |    | ||      | |||  |||  | |  | |  |||  | |  | |     || |     | |  |   |||          |||   |||||||||| || ||||| || ||||| ||||||||||  || ||||| ||||||||||| |||||| | |||||||||||||||||||| || |||||||
gttagtgctatgattattatgctcgttgcagtgtagccctcttgattctttatacagtatcctttgtatattttatgcttgtaatcttatgcccatttctatgtgttatggtacatagGATGTCACGCTCCATGATCTAGATGCTGCAAATGCTCGCCCTCAAGGAGGCCAAGATATATTGTCCATGATGGGCCAGATGATGAAACCTCGTAAGACTG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 5
gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
                        ||| |  | | | || |   ||| | ||  | |||||         ||  |              | |||||| |||| |||||||| ||||| || ||||| |||||||| |  || |||||||| ||||||||| | ||| | ||||| ||||||||||| ||   ||||||||
------------------------gtactaac-tgtgaaga--aagggtccagtttctcttcacacagcaagtgtg-------------ggtgtatgtagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG

upper sequence: GRMZM2G018697_T03 (Zea mays), 3'ss of exon 6
lower sequence: EFJ33466 (Selaginella moellendorffii), 3'ss of exon 5
gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
                                ||   |||   ||    | |   | ||  |||          |  |  |  |     | ||||| ||||| |||||||| ||||| || ||||| |||||||| |  || |||||||| ||||||||| | ||| | ||||| ||||||||||| ||   ||||||||
--------------------------------gtactaactgtga----tgaaagggtccagtttctc------ttcacacagcaagtgggtgtattcagGACGTCACACTGCATGATCTAGATGCTGCAAATGCGCGTCCTCAAGGTGGACAAGATATTCTTTCCATGATGGGACAGATGATGAAGCCGAAAAAGACTG

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|60340836|gb|DN207809.1|DN207809
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|61118430|gb|DN559391.1|DN559391
EST:     ATAAGAAAAAAGAAATAGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|87152471|gb|DY397260.1|DY397260
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|93284661|gb|EB676925.1|EB676925
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|61118429|gb|DN559390.1|DN559390
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATAGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|31612366|gb|CD568988.1|CD568988
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
EST: gi|213174323|gb|FM191608.1|FM191608
EST:     ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATAGTGCAG                         GATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC
genomic: ATGTTCCTATCCCCAAAGGTGAAGTCCATAAGAAAAAAGAAATTGTGCAGgtatcattct ... atgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG
                                    ttctcac  putative branch site (score: 2)
                            atctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttttaataagaattaatgcttgtatttgcgtctcaacatggaggcttcatgtgctcttgttctgaagaggatctaatcttctcaccgatgtatgcagGATGTCACACTTCATGACCTTGATGCAGCAAATGCTCAGCCACAAGGTGGCCAAGATATTTTGTCCCTTATGGGCCAGATGATGAAACCACGAAAGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - -tgcttgt
- - - - - - - - - - - - - - - - - - - acatgga
- - - - - - - - - - - - - - - - - - - - - - - -cttcatg