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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

Basic information

species Zea mays
transcript GRMZM2G137930_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g02310.1 (Oryza sativa), 3'ss of exon 3
ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcatagaa-gcgactcctat---tcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
  | | || |  | |||    |   |    |    ||     ||   | |   |||      | |||  || | | |  | | ||| | |   ||   || |||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||   |
--gctggtatttcacattacaccaagaatttctcgaccaaaagaaaaaaga--aaagagaggaaaaactctaacaaattgtgtctcttttctgtcacttgtcagGTCATTGAGATTCCTAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATAGTG

upper sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 3'ss of exon 4
--------ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
        |  | | || |||  |     |    | ||   |  || ||| |   | ||   | |   | | ||||    |   | || |||  | ||       |||||||| || ||||| || ||||||||||| || ||||||||||| |||||||| || ||  | || 
gatgatggccatct-tgacactgactcaacaacccacccatgttctgtctcacaaa-gccacattatgtgacaaagcaatactca-gccacttttgtttt-----cagGTCATCGAAATACCGAGAGGCAGCAAGGTCAAGTATGAACTTGATAAGAAAACCGGGCTCGTAAAA

upper sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA13G19500.2 (Glycine max), 3'ss of exon 3
ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgc-tcaaatgcttaag---aaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
|   |  |||    | |||  |  |      |     ||| |  ||| |   |  |    |||      || |||  | |||      |  | || |    |||||  | || |||   |  || |||||||| ||||||||||||||||| | ||||||||| || | |
catatcatgttgttcctgtgaccttaaattgttatgatttttattgcctctattgagaaattagacttgaatacttgt-gaaatattgctgaatcttg---cagGTGGTCGAAATAGGGAAAGGAAGCAAGGTGAAATATGAACTTGACAAAAGAACTGGACTTATTATG

upper sequence: GRMZM2G137930_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 3'ss of exon 3
ctgtttgtgtcaccc-atgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcata---gaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
    | |||  |    |      | |  |   |      ||   |  | |||     |  | ||  |||  || ||   |||   |   ||| |  | ||| ||||  |||| |||   |  || |||||||| ||||||||||||||||||||||||||||||||||||
--actagtgaaatttgacaaaattttcataaataaattgttagaaaccttgccttcttaatcaaccaaggttcttatttgaacatatgtctaatttt-tgc-agGTGGTTGAAATAGGGAAAGGGAGCAAGGTGAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

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|9742923|gb|BE519071.1|BE519071
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|91878963|gb|EB408920.1|EB408920
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|91870587|gb|EB400969.1|EB400969
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|9794549|gb|BE552857.1|BE552857
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|89252994|gb|DY624780.1|DY624780
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|23357487|gb|BU645136.1|BU645136
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGNTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|211153963|gb|FL101500.1|FL101500
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|78109928|gb|DV528343.1|DV528343
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|60400269|gb|DN233076.1|DN233076
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|22521401|gb|BU080212.1|BU080212
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|21432147|gb|BQ547637.1|BQ547637
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|6973370|gb|AW438064.1|AW438064
EST:     AGGTCCTGGTGCTCCAACCATATT-AACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: AGGTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|60396637|gb|DN229505.1|DN229505
EST:     CAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: CAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|71441944|gb|DR822994.1|DR822994
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|76923128|gb|DV169344.1|DV169344
EST:     CCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: CCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|22546627|gb|BU098938.1|BU098938
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|86471929|gb|DY238299.1|DY238299
EST:     GCCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAGGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|60397937|gb|DN230753.1|DN230753
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|23357695|gb|BU645344.1|BU645344
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|71445656|gb|DR826706.1|DR826706
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|91870563|gb|EB400947.1|EB400947
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|211043567|gb|FL332011.1|FL332011
EST:     AGGTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: AGGTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|74035433|gb|DT535921.1|DT535921
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|76287732|gb|DV027300.1|DV027300
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|20301303|gb|BQ164246.1|BQ164246
EST:     TGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: TGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|22472706|gb|BU037186.1|BU037186
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|31557952|gb|CD527164.1|CD527164
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|22133615|gb|BQ833806.1|BQ833806
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
EST: gi|71444627|gb|DR825677.1|DR825677
EST:     GTCCTGGTGCTCCAACCATATTCAACTGC                         GTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA
genomic: GTCCTGGTGCTCCAACCATATTCAACTGCgtaaggccac ... cctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgctcaaatgcttaagaaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG
                                     ctcctattcct  CT-rich tract
              ttaagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttgtgtcacccatgttcctctgctccttggcactttctgatgcatgctcaaatgcttaagaaagactcatagaagcgactcctattcctatgccagGTCATTGAGATACCAAGGGGCAGCAAGGTTAAATATGAACTTGACAAGAAAACTGGACTGATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA