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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctggcagtgggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

Basic information

species Zea mays
transcript GRMZM2G181151_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g37180.1 (Oryza sativa), 3'ss of exon 5
---tctggcagtgggtctgcccttttta-gtgttttcttcattaccctgtttattgtgaaaatcctgtcttgtttgat-tatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
        |  |  || |      ||||  | ||||| |  ||  | |||      ||||    | |  ||| || || | ||  |||     |  ||  || ||||  ||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||| ||||| |||||||| || || || || || |||||||
tgaataatctataagtttttgtagtttatatcttttccttgtttgcatgta-gcactgaagtagcggcattgcttaatatgtgtggta----attctttctatagGTCCTGAAAACTCCTGTCTCACTTGATATGCTTGGGCGCATTTTTAATGGATCTGGAAAACCCATTGATAATGGCCCACCTATTTTGCCAGAGGCCTACT

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA10G42940.2 (Glycine max), 3'ss of exon 5
tctggcagtgggtctgccctttttagtgttttcttcattaccctgt--ttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
| |  |  ||  | |   |||||   || |   || | |    ||   | | | |      ||| |    ||    | | |    | || ||||| |  |||||| || ||||||||||||||||| || |||||||| ||||| |||||||| ||||||||||| ||||| ||||| || || || |||||||| || ||| 
tttttctttgaattt---cttttacatgctacttttactgtattggaatcaatttattccaccttttaacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTAGACATGCTTGGACGCATATTTAATGGCTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA18G48280.1 (Glycine max), 3'ss of exon 5
tctggcagtgggtctgccctttttagtgttttcttcattaccctgttta---ttgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT-
        |   |    |||||||  | ||   |   | |   |||||      ||  || |  || ||    |  ||         ||||| ||| || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || || |||||||| || |||| 
-----tgattattgaatcctttttcattttgattctttgattttgtttgaatcagtttaactgttgactcccattttttccttaattattgtttttgttcacaggTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATTTTACCTGAGGCTTACTT

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA09G38110.2 (Glycine max), 3'ss of exon 5
tctggcagtgggtctgccctttttagtgttttcttcattaccctg-tttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
|     | ||  |||      ||| |  || | |   || |  || || | | | |   |    ||   |||  ||   || |  ||||| ||| || |||||| || |||||||| || ||| | || |||||||| ||||| || ||||||||||||||||| ||||| ||||| || || |||||||| || || ||||
ttgattattgaatctttttcattttg-attgtttgatttgctttgattcagtttaactgttgactcccattttttttctcaat-tattgtttttgttcacagGTGTTAAAAACTCCAGTATCATTGGACATGCTTGGCCGCATATTCAATGGTTCTGGAAAACCAATTGATAATGGTCCACCCATATTACCCGAGGCTTACT

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA20G24070.1 (Glycine max), 3'ss of exon 6
tctggcagtgggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtcttg--tttgattatgcagtacattgtgtttctt-acagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
| |  |  ||  | |   |||||   ||||   || |||    ||      ||  |   |   | |||  ||    | | |    | || ||||| |  |||||| || ||||||||||||||||| || |||||||| ||||| |||||||||||||||||||| ||||| ||||| || || || |||||||| || ||| 
tttttctttgaattt---cttttacatgttacttttattgtattggaatcagtttattccaccttttgacttcctcttttcctctctttttgtttgtccacagGTGTTAAAAACTCCTGTCTCACTGGACATGCTTGGACGCATATTTAATGGTTCTGGAAAACCAATTGATAATGGTCCACCAATTTTACCTGAGGCTTACC

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 5
------tctggcagtgggtctgc-cctttttagtgttttcttcatt-accctgtttattgtgaaaatcctgtcttgtttgattatgcagtac-attgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
      |     |      || |  |  |  ||  |||     |||        | ||||    | | |||  |  |    || |     ||   | ||| |||| |||||||||||||| ||||| ||| | || |||||||||||||| ||||| ||||| ||||| || ||||| |||||||| || ||  | || ||||| ||| 
gtaatttaccataaaaatccttcgtccctccagcatttcgcagatttgttgaaatgattggttgatttctgcttcctgcattttttttaaaccggtttgtgtctttcagGTTTTGAAAACACCTGTATCATTGGACATGCTTGGGCGCATATTTAACGGTTCAGGAAAGCCGATTGATAATGGCCCTCCTATTCTGCCAGAAGCATACC

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G38510.4 (Arabidopsis thaliana), 3'ss of exon 6
tctggcagtgggtctgccctttttagtgttt-tcttcattaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
                           |||| | ||   ||||  ||||      |  |   | | |  | |  | |     | || ||| |||   | ||||||||||||||||||| ||  | ||||||||||| ||||| || |||||||| || || || |||||||| || || || ||||| ||||| || ||||
---------------------------gtttgtttttgctaccaagttttaaagtatcagtgtctataatatactcacattttccaatgttttttccatagGTTTTGAAAACTCCTGTTTCTTTGGATATGCTTGGTCGCATCTTCAATGGTTCAGGGAAGCCCATTGACAACGGTCCACCTATATTGCCTGAGGCGTACT

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv03s0038g02760.t01 (Vitis vinifera), 3'ss of exon 5
-tctggcagt---gggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtct-tgtttgattatg-cagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
 ||  ||  |   | |  |||  | | |||| |    || |  | |   ||  || |     | ||||   | ||| ||| || |  |   ||    ||  |||||||||||||||||||||||||| | |||||||||||||| || ||||||||||| || ||||| ||||| ||||| || || ||||| || || || ||||
gtcaagcctttctgtgattgctatctctagtatcagtttgag-atcaacttctttct-----ttctgtagatatttcattgtgtccctttcttaccctttatacagGTTTTGAAAACTCCTGTCTCATTGGATATGCTTGGGCGTATCTTTAATGGTTCAGGGAAACCCATTGATAATGGGCCTCCTATATTGCCAGAGGCTTACT

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 5
-----tctggcagtgggtctgccctttttagtgttttcttca-ttaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
     |||   || |  | |  | ||  |  |    || ||| ||   |||  |||| ||  |||   |   ||||||  |  |  | | ||| ||||   | |||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||| ||||| ||||||||||| ||  | || || || ||| 
ctctctctacaagagcctttctctttacttttaacctcctcagtttgtctgaatattttggcaat---gaaatgtttgtctg-gttgaatattttgttg--tgcagGTTTTGAAAACACCTGTATCACTGGATATGCTTGGCCGCATTTTTAATGGTTCTGGAAAACCCATTGATAATGGCCCCCCAATTCTGCCAGAGGCTTACC

upper sequence: GRMZM2G181151_T02 (Zea mays), 3'ss of exon 5
lower sequence: PP1S85_75V6.1 (Physcomitrella patens), 3'ss of exon 5
tctggcagtgggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtcttgtttgattat------gcagtacattgtgtttct--tacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
           ||| |     | |  | ||||  |    | |  | ||     || |    | |  |  | ||||||      |||||   || |  || |  |  ||||  ||||||| || |||||  | || ||||| || || ||||| ||||||||||| |||||||||||||| ||||| || ||  |  | ||||| ||  
--------attgtccgaatgatattctatttttctatggatcgcggttgggccgacatgtgtttactactcgattatcgacctgcagttggttcttgttgtggtttagGTGCTGAAAACACCAGTCTCGTTAGACATGCTGGGACGTATTTTCAATGGTTCTGGCAAACCTATTGACAACGGCCCTCCAATTCTTGCAGAAGCTTATC

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|33102148|gb|CF062108.1|CF062108
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|211182799|gb|FL070450.1|FL070450
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|33102006|gb|CF061966.1|CF061966
EST:     GAACTTCTGAAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32908718|gb|CF013531.1|CF013531
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|33100953|gb|CF060913.1|CF060913
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|211182798|gb|FL070449.1|FL070449
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32945519|gb|CF050338.1|CF050338
EST:     GAACTTCTGGAATAGACAACAAATACACANCCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32933270|gb|CF038082.1|CF038082
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTTAATGG
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCA-TTTTTAATGG
EST: gi|67028686|gb|CO457435.1|CO457435
EST:     AACAAATACTC-CCCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: AACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32944897|gb|CF049716.1|CF049716
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACACGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|9953932|gb|BE640515.1|BE640515
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32846162|gb|CD985843.1|CD985843
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32933397|gb|CF038209.1|CF038209
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|33100729|gb|CF060689.1|CF060689
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|31664290|gb|CD573015.1|CD573015
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32942779|gb|CF047598.1|CF047598
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|13389395|gb|BG462701.1|BG462701
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|32931129|gb|CF035941.1|CF035941
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCGGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
EST: gi|211466593|gb|FL062044.1|FL062044
EST:     GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAG                         GTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT
genomic: GAACTTCTGGAATAGACAACAAATACACAACCGTGCAGTTTACAGGCGAGgtgcttcatc ... tttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT
                      gtttgat  putative branch site (score: 5)
                                           tgtttctt  putative PPT
                       tttgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctggcagtgggtctgccctttttagtgttttcttcattaccctgtttattgtgaaaatcctgtcttgtttgattatgcagtacattgtgtttcttacagGTTTTGAAAACTCCTGTCTCACTCGATATGCTTGGGCGCATTTTTAATGGTTCTGGAAAACCTATTGACAATGGCCCCCCGATATTACCTGAAGCCTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC