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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagccctcctcaaccttatgcccatttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

Basic information

species Zea mays
transcript GRMZM2G018228_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G38520.1 (Glycine max), 3'ss of exon 2
--------------gttagccctcctcaaccttatgcccatttgaattgcttcattctgaggat--acgcccctgat-tatt---attgttctatatt-agGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                |     |  | |   ||||   |  || ||||  |  | | || | ||  |      || | | ||    |  || | | || ||| |||||||| ||||| ||||| || ||||||||||| ||||| || |||||||| ||  |||| || |||||||| || ||||| |||||||| || ||
gtatatctctcagtaatcaaagtttttatttttattttctgtttaattattatagtttgtgtattgaaattgttgttgtgttcgggtgattttttgtttagGATACATTGGAGAGTTTGAGTATGTTGATGACCACAGGGCTGGTAAAATCGTGGTTGAATTGAACGGTAGACTGAACAAGTGTGGGGTTATTAGTCCCCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G02200.1 (Glycine max), 3'ss of exon 2
--------gttagccctc-----ctcaaccttat-gcccatttgaatt--gcttcattctgaggatacgcccctgattattattgttctatat-tagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
         ||||   ||      |  |  ||||     ||||  |||  | ||   | |    | | ||   ||  |     || | ||| | |||| ||||| || ||||| ||||| || ||||||||||| ||||| || |||||||| ||  |||| || |||||||| || ||||| |||||||| || ||
gtatatctcttagtaatcaaagttttgattttattatttatttttatttagtttgtgtattgaaaaatgctgttgtgttcggatgatttatgtgtagGATACATCGGAGAGTTTGAGTATGTTGATGACCACAGGGCTGGTAAAATCGTGGTTGAATTGAACGGTAGACTGAACAAGTGTGGGGTTATTAGTCCCCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G00600.2 (Glycine max), 3'ss of exon 2
--------------------gttagccct-cctcaaccttatgcccatttgaattgcttcatt-ctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                     | |      |||  |  | |     ||  |||||| || | |  ||  |  | |        |  | | || || | | ||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||||| ||  |||||||  | |||||||| ||||| ||||||||||| ||
gtattgatttgttatgtaatatgaatttggccttgaattgaatataataggaattgttttagtgttgttggcatgttttgttatggtgtggtgctttgt-agGGTACATTGGTGAGTTCGAGTATGTTGATGACCACAGGGCTGGGAAAATCGTGGTTGAATTGAATGGGCGGCTGAATAAGTGTGGGGTTATTAGCCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G45060.1 (Glycine max), 3'ss of exon 2
-------------------------------gttagccctcctcaaccttatgcccatttgaa--ttgcttcatt-ctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                                 ||       | ||  | ||    | | | |  ||| |||| |  ||  |  | |        |  | | || || | | ||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||||| ||  ||||||| || |||||||| ||||| ||||| ||||| ||
gtatttctcaacacctctatttttgttcccccctaattgaattgaatataatagataataggaacttgtttcagtgttgttgtcatgatttgtgatggtgtggtgctttgt-agGGTACATTGGTGAGTTCGAGTATGTTGATGACCACAGGGCTGGGAAAATCGTGGTTGAATTGAATGGCAGGCTGAATAAGTGTGGGGTTATAAGCCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G00590.2 (Glycine max), 3'ss of exon 2
--------------------gttagccct-cctcaaccttatgcccatttgaattgcttcatt-ctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                     | |      |||  |  | |     ||  |||||  || | |  ||  |  | |        |  | | || || | | ||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||||| ||  |||||||  | |||||||| ||||| ||||||||||| ||
gtattgatttgttatgtaatatgaatttggccttgaattgaatataataggaatttttttagtgttgttggcatgttttgttatggtgtggtgctttgt-agGGTACATTGGTGAGTTCGAGTATGTTGATGACCACAGGGCTGGGAAAATCGTGGTTGAATTGAATGGGCGGCTGAATAAGTGTGGGGTTATTAGCCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G10950.1 (Glycine max), 3'ss of exon 2
----------gttagccctcctcaaccttatgcccatttgaattgcttcattctgagg-atacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
          ||||  | || |     | ||      |  | ||| ||  |  ||    ||  |    ||  | | |||||  | |  |||| |||||||| ||||| |||||||| ||||| ||||||||||| || || || || ||  ||||||| |||||||| |||||||| |||||||| || ||
gtatttgtttgttaatcttcttttttttaataatagctcaatttggttactcttggttcatctgtttttgcct-tgattgtgtttt-ctagGGTACATTGGAGAGTTTGAGTACGTTGATGATCACAGAGCTGGAAAAATTGTTGTTGAATTGAATGGTAGACTGAACAAATGTGGGGTTATTAGTCCGCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: AT5G59850.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagccctcc----tcaaccttatgccca---tttgaattg--cttcattctgaggatacgcccctgatt----attattgttctatat-tagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
    |||   ||| |    |  | || ||   ||   |||| | |   ||| |||||| |  |   |  ||| ||    ||| ||| |  |  |  |||||||||||| ||||| |||||||| |||||||||||  |||| ||||||||||| ||||| ||||||||||| || |||||||| || || || || ||
gtatgttgatcctgcattgtttagctcattttcacattttgtaataaccttgattctgtgtttgatcaactgttttaacatttttgatgaaactgcagGTTACATTGGTGAGTTTGAGTACGTTGATGACCACAGGTCTGGAAAGATCGTGGTCGAGCTTAATGGAAGACTTAACAAATGTGGAGTCATCAGTCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: AT2G39590.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------gttagccctcctc------aaccttatgcc-catttgaattgcttcattctgaggatacgcccctgattattattgttctatat-tagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                                                                     |||  ||   ||      ||| || ||     | | || || |   || |||    |  | |   |   || |  ||   | | ||||||||||||  ||||| || || |||||||| |||||| | |||||||| ||||| ||||| |||||||| || || || || ||||||||||| || ||
gtacaattgttttactcaatgagcttcttcttgtttgatttctctcttttttttttaggtttaagggaattataccgtatcgaataaaacattctggaatctctcaaatgttcagttttgacttgaaacacacaaactttttcctttggtttatagGTTACATTGCAGAGTTTGAATATGTGGATGATCACAGATCCGGGAAGATTGTGGTTGAGCTTAATGGAAGGCTTAACAACTGCGGTGTTATTAGTCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: AT1G07770.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagccctcctcaaccttatgcccatttgaattgcttc-attct--gaggatacgcccctgattat-----tattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
    | |   ||  |   |  ||||    ||    ||| ||   |||||  || | |   ||    |||||     ||    || |    |||||||||||| ||||| ||||| || |||||||||||| |||| |||||||| || ||  |||| |||||  |||| || ||||||||||| ||||||||
gtatgattatcccaccagattttatata-atagagattcctaagattctcggatgttgttccttaaattatgtggttaccaatcaaatgcagGTTACATTGGTGAGTTTGAGTATGTCGATGACCACAGATCTGGCAAGATCGTCGTTGAATTGAACGGAAGGTTGAACAAGTGTGGTGTTATCAGCCCACG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: AT3G46040.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagcc-ctcctcaaccttatgcccatttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
    | |||   ||   ||    ||    | ||||| || ||  || |  ||  | |     | || ||  || ||   | |||||||||||||||||||| ||||| || |||||||||||  |||| ||||| || || ||||| |||||||| ||||| || ||||| ||||| || || ||
gtatgctagtaactttgcagagctag---cgtttga-ttcctgtatac--agttttcaagtgtaatgatgcttcttggtttttagGTTACATTGGCGAGTTTGAGTATGTTGATGACCACAGGTCTGGTAAGATTGTTGTTGAGCTTAATGGAAGGCTGAACAAGTGTGGAGTTATCAGTCCTCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: Vv13s0019g00530.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------gttagccctcctcaacctta---tgcccatttgaattgctt-----cattctga---ggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                                          |   | || | |   ||    ||    |||   || | |     |||| | |      ||     |||||| ||||| | || ||  |||||||||||| ||||| ||||| || ||||| |||||  |||| ||||| || || || |||||||||||||| || |||||||| ||||| || || ||
gtactaatcaattcatttgaatttcagattgtttcaattttcttttcttctttacttttgcattgtttttttttgttacctgtgtacatttttattcacgtattttactgatt-ttattttgctctac-agGTTACATTGGAGAGTTTGAGTATGTTGATGATCACAGGTCTGGAAAGATTGTTGTTGAACTGAATGGAAGACTAAACAAATGTGGGGTTATCAGTCCCCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S1_304V6.1 (Physcomitrella patens), 3'ss of exon 1
----------------gttagccctcctcaa--ccttatgcccatttgaat--tgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                ||| |  |   |     | |||     |   ||||  |||    ||      | | || | |   | |   |  ||  |   ||| || ||||| ||||| ||    || |||||||||||||| ||||| ||||||||||||||||| || ||| |||| || || |||||||| || || ||
gacacatgccttttatgttggaacgaattgtttctttaaatgtaaaagaatcctgcggatttacactaacatgcacttttctgtatgtcatccctcgcagGATATATTGGAGAGTTTGAACTGGTTGATGACCACAGAGCGGGGAAAATCGTGGTGGAGCTGAACGGTAGATTGAACAAGTGCGGTGTTATCAGTCCCCG

upper sequence: GRMZM2G018228_T04 (Zea mays), 3'ss of exon 2
lower sequence: PP1S115_101V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------gttagccctcctcaaccttatgcccatttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                          |     |  |  | |    | || ||| |   |||| |  |||| | |   |   | |    ||    |  || | ||| |||||||| ||||| ||    |||||||||||||| || ||||| || |||||||||||||| || ||  |||| || |||||||| || || || ||
taatagtaagggaacatgtaacgtagtcatgttggtggatcgagcgtcc-tttcatgagcttgaacctgacgtt---cttttaaaatatacatattcatttcagGCTACATTGGAGAGTTTGAACTTGTGGATGACCACAGGGCAGGGAAAATTGTGGTGGAGCTGAACGGCAGGTTGAACAAGTGTGGTGTGATCAGTCCCCG

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|24934676|gb|CA452894.1|CA452894
EST:     GCCGTCATCCAAGG-GATCATCAAGTTCCTGACGGTCATGCAGCGCCATG                         GCTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
genomic: GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctc ... tctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
EST: gi|18384865|gb|BM418064.1|BM418064
EST:     CCGTCATCCAAGGATAAACATCAAGTTCCTGACGGTCATGCAGCGCCATG                         GCTACATTGGTGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
genomic: CCGTCATCCAAGG-TGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctc ... tctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
EST: gi|18384866|gb|BM418065.1|BM418065
EST:     GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATG                         GCTACATTGGTGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
genomic: GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctc ... tctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
EST: gi|18384863|gb|BM418062.1|BM418062
EST:     GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATG                         GCTACATTGGTGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
genomic: GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctc ... tctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG
EST: gi|16746125|gb|BM032555.1|BM032555
EST:     GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATG                         GCTACATTGGTGAGTTCGAGTACGTGGATG-CCACAGAGCTGGGAAGATCG
genomic: GCCGTCATCCAAGGTGATCATCAAGTTCCTGACGGTCATGCAGCGCCATGgttagccctc ... tctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG
                             ccctgat  putative branch site (score: 4)
                                         ttgttct  putative PPT
                                tgattattattgttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagccctcctcaaccttatgcccatttgaattgcttcattctgaggatacgcccctgattattattgttctatattagGTTACATTGGCGAGTTCGAGTACGTGGATGACCACAGAGCTGGGAAGATCGTGGTGGAGCTGAATGGAAGACTGAATAAATGTGGTGTTATTAGCCCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA