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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttgaacatctatgaaatttatgaagagctaatcttttttcaaggataatacctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG

Basic information

species Zea mays
transcript GRMZM5G825524_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 3
ctcttgaacatctatg-aaatttatgaagagctaatcttttttcaag-gataatacctatgatttatgaaaacatacatctgatttggtgtt---tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
      | |||   || |  |  |    ||  | || ||   |||   || | | |  | ||  | | |    ||  | |||||||||||||    |  | | ||||||||||| ||||| || |||||||||||||| ||||| |||||||||||||| ||||| ||||||||||| || ||||||||||| |||||||| || 
-----aatcatgcttgcatgtacaatgggatgtgattttgactcatttgaaattgctgaagaactgttatggtatgaacctgatttggtgttgttcatgtcctagCTATCTCCTCTGCACAGTAGGATCTGTGTACATTAAATCAAAAGAGGCTCCTGCGAAAGACGTTCTTAAAGACCTTGTTGAAATGTGTCGAGGCATCCAA

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 3
-ctcttgaacatctatgaaatttatgaag----agctaatcttttttcaaggataata--cctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
    || ||    |   | ||||     |    ||   |  || |||| ||  |||||  | | | | || |||       |   | ||||  || || |    ||| |||||||| || || || ||||| || ||||||||||| || || |||||||| || ||||||||||| |||||||| || ||||| ||||||||||||
ggggtttaatgctttgaagatttgcagtggttaagtgtacattctttcgagtttaatatgcttcttacttgtgag------ctgttaattttatgattgcg-atcagGTATCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTCGTGGAGATGTGTCGAGGCATTCAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G08390.1 (Glycine max), 3'ss of exon 3
ctcttgaacatctatgaaatttatgaagagctaatcttttttcaaggataatacct--atgatt--tatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
    |||  |    | ||  || |||||   |   | |  || |    | || | |  ||| ||  ||||        |   | || |  || || ||   ||| || ||||| || || || ||||| || ||||||||||| || || |||||||| || ||||||||||| ||||| || || |||||||| |||||||||
--agtgagaagggtttaatgttctgaagt-tttgccgtgcttaagttttcattctttcatgtttaatatgcttgtgagctgttaatattatgattgca-atcagGTACCTCCTCTGTACAGTAGGATCAGTATACATCAAATCCAAGGAAGCTCCTGCAAAGGATGTTCTTAAGGATCTTGTGGAGATGTGCCGTGGCATTCAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 3
ctcttgaacatctatgaaatttatgaagagctaatcttttttcaaggataat-acctatg-atttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
   ||||  |    |  |  ||   |  |  |  |||  | |  ||  |  | || | |  |  ||    || ||   |    |||  | |       | || |||||||| || || |  ||||| ||||| |||||| | || || |||||||| || ||  ||||||||||||| ||||| |||||||| || ||||||
--tttgattactacttgatgttgctagcatttcttctgatatttagtctgttcacttctctagctaaagtaatatttgttcattttattttcccttccctagGTATCTCCTATGTACAGCAGGATCCGTGTATATCAAAACCAAGGAAGCTCCTGCCAAGGAAATTCTTAAAGATCTTGTTGAGATGTGCCGTGGGATTCAG

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g14680.t01 (Vitis vinifera), 3'ss of exon 3
ctcttgaacatc----tatgaaatttatgaagagctaatcttttttcaaggataatacctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
  ||||||  |     | |    | ||||      ||  |  |||| ||  ||   | ||   |||   ||  | ||  ||   || || |||| |  |  ||| |||||| | || ||||| |||||||| || |||||||| || ||||||||| |||| ||||| ||||||||||| || ||||||||||| || ||||| 
-gcttgaagtttgtattttagtctgtatgttagcatatgcaatttttaaatatgccatctccaattctagagcatatgaat---atgtgttgttgatttatcagGTATCTCTTATGTACGGTAGGATCTGTATATATCAAATCAAAGGAGGCTCCTCCTAAGGATGTCCTTAAAGATCTTGTGGAAATGTGCCGTGGTATTCAA

upper sequence: GRMZM5G825524_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 3
ctcttgaacatctatgaaa------tttatgaagagctaatcttttttcaaggataatacctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
   ||| ||||    || |      ||| |  | |  |    |||||||| | |   |  | |||  |||    |   |  ||    | || | | ||    |||| ||||| || || || || |||||||||||||||||||| || |||||||||||||| ||||||||||| ||||| || ||||||||||| ||||| || 
ggattgtacattatagagacatcagtttgtataaatttttatttttttcatgtaatgtttccatgtctta----attttgaattc--tgtgttctctattgcccagGTATCTTCTCTGTACAGTTGGATCTGTGTACATCAAATCTAAGGAGGCTCCTGCTAAGGATGTTCTTAAGGATCTTGTGGAAATGTGCCGTGGCATCCAA

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|211323478|gb|FL043268.1|FL043268
EST:     GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACT                         CTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
genomic: GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACTgtgagcctgc ... tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
EST: gi|18659312|gb|BM500271.1|BM500271
EST:     TTGATATGTACGAGCTTGTGCAGCATGCTGGGGAATGTCTTACCGAGACT                         CTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGANGCTCC
genomic: TTGATATGTACGAGCTTGTGCAGCATGCTGGG-AATGTCTTACCGAGACTgtgagcctgc ... tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
EST: gi|19351762|gb|BM896294.1|BM896294
EST:     GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACT                         CTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
genomic: GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACTgtgagcctgc ... tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
EST: gi|22491272|gb|BU051195.1|BU051195
EST:     GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACT                         CTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
genomic: GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACTgtgagcctgc ... tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
EST: gi|18964924|gb|BM661289.1|BM661289
EST:     GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACT                         CTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC
genomic: GTTGATATGTACGAGCTTGTGCAGCATGCTGGGAATGTCTTACCGAGACTgtgagcctgc ... tacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataatacctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG
                              atctgat  putative branch site (score: 4)
          tatgatttatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttgaacatctatgaaatttatgaagagctaatcttttttcaaggataatacctatgatttatgaaaacatacatctgatttggtgtttacatgccagCTATCTCCTGTGCACGGTGGGATCTGTGTACATCAAATCGAAAGAGGCTCCTGCTAAAGATGTTCTTAAAGATCTCGTTGAAATGTGCCGAGGCATTCAG

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