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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA

Basic information

species Zea mays
transcript GRMZM2G116151_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
-------------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
              ||   ||| ||| |     ||||  |  | |||   ||| ||| ||||||   ||  ||| |||| || |||| |||| ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||
gtcagctcttctaatccggatgtctttttc---atttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 2
-----------------gtctttatgccttctc---tggaatttttaattgtaattcatcgtagctgcattagcataaacgtttt----ttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
                 || || ||   |  |    |  |   | ||    | || |||  | | |   |    ||  |||| ||    | || ||  ||||| ||  | |||||||| ||| ||| |||||| || ||||| |||||  |||| ||||||||||| ||||||||
gtatggtgttggttagtgtgttgatatttatttggttaaagagtgtatgatttatgcatattggatttgtcgttattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
-------------gtctttatgccttctctggaatt---tttaattgtaattcatcgtagctgcattagcataaacgtttt----ttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
             || || ||   |  |     | |   ||| ||||  || |||  | | |   | |  ||  |||| ||    | || ||  ||||| ||  | |||||||| ||| ||| ||||||||| ||||| |||||  |||| ||||||||||| ||||||||
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattg--atgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
-----------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
           || |||     ||  || |  || ||  | ||  |   |  |   |    |    |  | || |    |  |  ||||| ||  | || ||||| ||| ||||||||||||| || ||||||||  | || ||||||||||||||||||||
gtatgctgtttgtgtttgcaagtttacttgctttcttt-tggttttctgtgatctgtaatgtgattttgatgtgtccacttttg-tagGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
-----gtctttatgccttctc--tggaatttttaattgta---attcatcgtagctgcattagcataaacgtttttt------ttcata----ctagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
        |||||| |||     |  |||   | | |||    ||  ||  | | |    |    | ||  | ||||      |||||      ||||||||  | |||||||| ||| ||| ||||||||| ||||| |||||  | || ||||||||||||||||||||
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------gtctttatgccttctctggaatttttaa--ttgtaatt----------catcgtagctgcatt------agcataaac---gtttt-ttttcatact---agGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
                              ||| |   |  |||  |  | |    |   |||| |||           ||| | |||   |       || | ||||   || || ||||| | ||   |||| ||  | || ||||||||||| | |||||| |||||||| |||||| ||||||| |||||||||||||||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgtt---ttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
                                                               |||  ||      ||  |   || | |||    || |  |||      || | ||  |  ||    |  ||  | | |||||||  | || || || ||||| |  || || || ||||| |||||| |||||||||||||||| ||||||| 
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatt----tttaatgtaataagttttgtattcatattgaactcgtttgtgc-agGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
     ||  |  |     || ||  | | |   |||     |     ||   || | | |     | ||      |||||||  | || ||||||||  ||| ||| ||||| |||||||||||  |||| ||||||||||||||||||| 
----gtagactgttcgaagatttgctcagttggattggctcttttctcagcggc-tgatcaaagatgtt---gtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ19085 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
   |   || | | ||     | ||   || |   | ||  |   ||  |||     |||| |  ||| |     |||||||  |||| || || ||| | | |||||||||||||||||||||  ||||||| || ||||| |||||| |
--gtcggtggcgtttcc----tcttctttttttgcttatgctgattgtgtta----taacgctcgtttgcgc---agGTTGCTCTCAAGTTCGAGCATAGGAGCAGCAAAGGTTGCAACTATGGGCCTCCTTACGAATGGCAGGTTTACGA

upper sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
     ||  |  |     || ||| | | |   |||  || |  || ||   || | | |     | ||      |||||||  | || ||||||||  ||| ||| ||||| |||||||||||  |||| ||||||||||||||||||| 
----gtagactgttcgaagattttctcagttggattgctcttttct-cagcggc-tgatcaaagatgtt---gtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|30306558|gb|CD001231.1|CD001231
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|101387539|gb|EB815784.1|EB815784
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|211200248|gb|FK978072.1|FK978072
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGTGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|71767696|gb|DR965633.1|DR965633
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|78112677|gb|DV531071.1|DV531071
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|211200247|gb|FK978071.1|FK978071
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|149078987|gb|EE167841.2|EE167841
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
EST: gi|30031898|gb|CB833749.1|CB833749
EST:     TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAG                         GTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT
genomic: TTTCCTCTCCTAGTGTTAGTGACAGGACGCCCGGTGCGAATGCTTTAGAGgtctttatgc ... ttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA
 ttttaat  putative branch site (score: 3)
                                       ttttttttcatact  putative PPT
                                ataaacgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG