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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG

Basic information

species Zea mays
transcript GRMZM2G421857_T02
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 11
tgatatgggtgcctctttcagtttgtcagctgtatttc---tgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtacc-ttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
     ||  |   || ||  |  ||  |  |||||||      | |   | |  |||     ||  |  |  |||  |  || || ||    |||    | |||||||||| || |||||||||| |||||| ||||| ||||| ||||| ||||||||||| |||||||| || |||||||||||||||||||| || || ||
----ttgctttggtcatttggactgctatatgtattttatggaccttaagttcatcaccaatgatctcattgtaaacaaaatcttatatgactttgccccccagGAATTACGATAGCTGAGTATTACCGTGACATGGGTTACAATGTCAGCATGATGGCTGATTCCACCTCACGATGGGCTGAGGCATTGCGTGAAATTTCTGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 12
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcaga-gtttctgttaacaatcatgttgtaccttttttaact-cagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
  ||||  |  | |       ||  | |  ||| |  | |  ||  ||||   |||    |   |  | || | ||| || ||     ||||| || | ||||||| ||| | |||||||||||| | |||||||| || || |||||||||||||| || || || ||  | ||||| || ||||||||||| ||||| ||
-tatatttgcccttaaaatgattaatgaattgtttgaccgtgtgctgcttgagagttttaacactgattttgataat-atatttcttttttttcaattgcagGAATCACATTAGCTGAGTATTTCAGAGATATGGGTTATAATGTCAGTATGATGGCAGATTCTACATCTAGATGGGCAGAAGCATTGCGTGAAATCTCTGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 12
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
          |     |||||     ||| | || |  |  |||  |  |  || |||  | |     ||     |  | || |    | |  |   ||||||| ||||| ||||| |||||  | |||||||||||||| || ||||||||||| ||||| || ||||| ||||| || |||||  | || || |||||
----------gtaatgttcaggcacacagatttaatagttattgatgaatcccattgccta-tgctcattttttttttttttttttaatgtgaattccagGAATCACAATCGCTGAATATTTTAGAGATATGGGCTACAATGTTAGTATGATGGCAGACTCAACTTCCCGTTGGGCAGAAGCATTAAGAGAAATTTCAGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 12
-tgatatgggt-gcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
 |   || ||| || | |||  | |         | ||||    | | |  | |   | || | ||  | |  | |   ||||  |  | |       ||||| || |||||||| || || ||  | || ||||| ||||| |||||||||||||| || || || || || ||||||||||| ||||||||||| || ||
tttccattggtagcttttttttggtgaagcaacatttttccaagttttgtatatttattcaaaattattttctaaaccaatgtgat--catggaatgttcagGTATCACAATTGCCGAATACTTTAGAGACATGGGTTACAATGTCAGTATGATGGCAGATTCAACATCTCGTTGGGCTGAGGCTTTGCGTGAGATATCTGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 12
--tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
  |||      |     | |  || | ||| || | | |   |||||   |     |||| ||| |  ||||  | | |   |   |   |   |   ||||| || || || ||||| || ||| | |||||||||||||| || ||||||||||| || || || || || ||||| ||||||||||| || || |||||
cctgaagcttttagtggtctt-gtctatcacctttgtgttaccttgtta-tggaaggtgctgagatgatgttctccaactaatatgattgtgggtttttcagGTATCACTATAGCTGAATACTTCAGAGATATGGGCTACAATGTTAGTATGATGGCAGATTCAACATCTCGATGGGCAGAGGCATTGCGAGAAATATCAGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------tgatatgggtgcctctttcagtttgtc-agctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
                                    || | |  |   |  |||||   | |   | ||| |       | ||   | | |  ||| | || |   | |  ||     ||    |||  |    |||| || ||  | || || || ||| | |||||||| ||||| |||||||||||||| ||||| || || || |||||||||||  | |||||||| || ||
gttattttcttttcttctgagactctactttctaggtgctgtatgaaaccatttcatcctctttggatgtttgaaatgctatcctgtatgatcgcatacttccgcatcattatgcaaatgc-tgtttcctgttgcagGTATCACTTTGGCAGAATACTTCAGGGATATGGGTTACAATGTCAGTATGATGGCAGACTCTACATCTCGCTGGGCTGAGGCGCTTCGTGAGATTTCTGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 11
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
                                          | |  | || || | |||        | | |  | || || |   |  |||    |||| |||||  | ||||||||||||||||| |||||||| || |||||||||||||||||||| || ||  | ||||| || || |||||||| || || ||
-----------------------------------------gtatgtccttccaattcaggc------tcagcgctgattttatcgatggttt----cagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

upper sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 12
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
                                          | |  | || || | |||        | |||  | || || |   |  |||    |||| |||||  | ||||||||||||||||| |||||||| || |||||||||||||||||||| || ||  | ||||| || || |||||||| || || ||
-----------------------------------------gtatgtccttccaattcaggc------tcaacgctgattttatcgatggttt----cagGCATTACTCTGGCTGAGTATTTCCGTGACATGGGCTATAATGTCAGTATGATGGCTGACTCGACGTCGAGATGGGCCGAAGCCTTGCGTGAAATATCCGG

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|67026160|gb|CO454909.1|CO454909
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|31360193|gb|CD444550.1|CD444550
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|51592889|gb|CV072035.1|CV072035
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|61118945|gb|DN559906.1|DN559906
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
EST: gi|6012344|gb|AW061700.1|AW061700
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTG                         GAATTACAATTGCT
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCT
EST: gi|19437277|gb|BM953687.1|BM953687
EST:     TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACAG                         GAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA
genomic: TAACACATCAAACATGCCTGTCGCTGCTCGTGAAGCTTCCATTTACACTGgtaaaaccct ... tttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG
                                            ttttaac  putative branch site (score: 2)
                                      tacctttttt  CT-rich tract
                                          ttttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatatgggtgcctctttcagtttgtcagctgtatttctgcttgtcgcttttcagtgcagagtttctgttaacaatcatgttgtaccttttttaactcagGAATTACAATTGCTGAGTATTTCCGTGATATGGGCTACAACGTCAGTATGATGGCTGACTCCACCTCCCGGTGGGCTGAGGCATTGCGTGAGATCTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC