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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

Basic information

species Zea mays
transcript GRMZM2G053764_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.3 (Glycine max), 3'ss of exon 1
-----------tctcttggtctgttttccaattctgc-----ctgaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
           | ||    | | ||||     | | |     | ||  |||||||  |||| |   || |||  | |  |||||   |  | | |   |||   |  ||| |     |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtctgtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcagGTCATCAGGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA08G01940.2 (Glycine max), 3'ss of exon 1
-------tctcttggtctgttttccaattctgc-----ctgaccgtgttctgcttgcttttttttttga-tctggccattcttgccg-gctttcttggttt--atcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
       | ||    | | ||||     | | |     | ||  |||||||  |||| |   || |||  | |  |||||   |  | | |   |||   |  ||| |     |||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||| || |||||| | || ||    || |
gtgatcttttccgaattttttttttgtattttcgatttcagaaagtgttct-tttgcataaattgttgtctttttccatttggggtgcgttggattgacatggatcaggtcatcagGATGATGAGTGATTACAAGGTGGAGACGGTCAACGATGGCATGCAAGAGTTCTTTGTGGAATTCCACGGACCCAAAGACA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA09G39370.4 (Glycine max), 3'ss of exon 1
tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtc-gcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
    ||  ||  || ||      | | | |  || |||    |  ||| |  |  | |||   | |  ||   ||   |||| || | | |   || | ||||||||||| || ||||||||||||||| | || ||||| ||||| ||||| |  ||  ||||| | || ||    || |
---gttaatcctttctctctcaattcatcaaagt-ttcaatcttttttctaatggggtctcttcctgattctgggtcctctttgtcttttgttttccgtagGATGATGAGTGATTACAAGGTCGAGATGATTAATGATGGAATGCAAGAATTTTATGTGCAATTCCATGGACCCAATGACA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: AT1G63800.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------tctcttggtctgttttccaattctgcctgaccgtg--ttctgcttgctttttt--ttttgatctggccattcttgccggctttcttggttta--tcggcgtcg-----cagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
             ||||  | | || ||   || | | |||   ||   || | ||  |||| |  | ||  | |||| |||     ||  ||| |||   |   | |  ||        ||||||||||| ||||||||||| |||||| | || ||||| ||||| || ||||| ||||||||||  || ||    || |
gtaatttttttaatcttattatcttatcagtttattcttgattttgagctccgattttttttctaatgtttgtttggcgatttgattcgatttttttgtgatgatttgatgtgagagtttagGATGATGAGTGACTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTTTGTCGAATTCAGTGGACCCAAAGACA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
-tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttat-cggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
   |  || | || || |   |  ||   ||    || | | |||     |       |   |   || |  | | |  |    |  | |  |     | ||||||||||| ||||||||||||||||||||||| ||||| |||   |||||||  || || ||  | || |||   || |
ggattgtgttgtgattacttttcttgttcgaattggtgcggtttggggaatcggcaagtt--gttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
---------------------------tctcttggtctgttttccaat---tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                             || |  |  | | |||| |   | ||    |||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: GRMZM2G053764_T02 (Zea mays), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
--------------------tctcttggtctgttttccaat-tctgcctgaccgtgttctgcttgcttttttttttgatctggccattc-ttgccggctttcttggtttatcgg----cgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
                      | |   |   || | |  | ||     ||||    | |  | ||||| ||  |   ||||   |||| ||||    | | || | ||  |      | |  |||||||||||| ||||||||||| |||||||| |||||||||||| | || ||    || || ||| | || ||    || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctc--tctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|32859163|gb|CD998844.1|CD998844
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|94476395|gb|EB705353.1|EB705353
EST:     TCCCAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     AAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGAGCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: AAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|32859162|gb|CD998843.1|CD998843
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     CCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: CCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|32859414|gb|CD999095.1|CD999095
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|211174889|gb|FL306344.1|FL306344
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     AAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: AAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     GTCCCCGAGCAAGCGCCGCGAGATGGACCTCATGAAGCT                         GATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATT
genomic: GTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|211174894|gb|FL306349.1|FL306349
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCT                         GATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT
genomic: TCCAAGATGTCGTCCCCGAGCAAGCGCCGCGAGATGGACCTTATGAAGCTgtgaggatgc ... ggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA
      ttttgat  putative branch site (score: 4)
     tttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTCGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

- - - - tctgttt
- - - - - - - - - - ttctgcc
- - - - - - - - - - - - - - - - -tgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg