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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaccaaccaattatttagctgttccctgtcttcggcatagccactgccattcaatgaatgttcacatctaatggttttactcttctgcttggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATTGCATGTGTTGGTGAGACCCTTGAGGAGAGGGAGGCTGGTTCAACCATGG

Basic information

species Zea mays
transcript GRMZM2G018177_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018177_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g05490.2 (Oryza sativa), 3'ss of exon 4
acaccaaccaattatttagct-gttccctgtcttcggcatagccactgcca--ttcaatgaatgttcacatctaatggttttactcttctgcttggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATTGCATGTGTTGGTGAGACCCTTGAGGAGAGGGAGGCTGGTTCAACCATGG
  || ||    | || | | | | | |   |    ||   | |  |||  |  ||     |   |   |||||||||||||    ||  | | || ||  ||||||||||||||||| || || | ||| || ||||||||  | |||||||||||||||||||||||||| || ||| || ||||  ||||||| |||||||
-tacaaa--ggtgatcttgttcgctacaaattggtggatgatctgctgtgaggttttcgtatcataatcatctaatggtttcctgctctttcctgaattgcagTTTGTTGGAGACAAAGTGGCATATGCGCTCTCTCAGGGCTTGAAGGTCATTGCATGTGTTGGTGAGACTCTCGAGCAGCGGGAATCTGGTTCGACCATGG
















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|13382324|gb|BG458999.1|BG458999
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|18162555|gb|BM332394.1|BM332394
EST:     GGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: GGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|32908102|gb|CF012915.1|CF012915
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|30087627|gb|CB885833.1|CB885833
EST:     TCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|60352667|gb|DN219640.1|DN219640
EST:     GAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTG-TGGAAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCAT
genomic: GAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGG-AGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCAT
EST: gi|18165365|gb|BM335204.1|BM335204
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|211519675|gb|FL104729.1|FL104729
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|76012320|gb|DT939490.1|DT939490
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|18165667|gb|BM335506.1|BM335506
EST:     GCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: GCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|91874218|gb|EB404175.1|EB404175
EST:     TGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|211522699|gb|FL104754.1|FL104754
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|84908490|gb|DW404368.1|DW404368
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTATGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|24765545|gb|CA400704.1|CA400704
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|61118536|gb|DN559497.1|DN559497
EST:     TCACTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTATGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|22819873|gb|BU499963.1|BU499963
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|60341170|gb|DN208143.1|DN208143
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|60397817|gb|DN230633.1|DN230633
EST:     AGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: AGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|211534317|gb|FL091476.1|FL091476
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|9733498|gb|BE512130.1|BE512130
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|17929542|gb|BM266502.1|BM266502
EST:     AGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: AGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|18175195|gb|BM350583.1|BM350583
EST:     GCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: GCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|76013518|gb|DT940688.1|DT940688
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
EST: gi|91056160|gb|EB166578.1|EB166578
EST:     TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAG                         TTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT
genomic: TCATTCTTGGACACTCTGAAAGGAGAGCTCTGCTGGGAGAATCAAATGAGgtatgatcca ... tggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccattcaatgaatgttcacatctaatggttttactcttctgcttggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATTGCATGTGTTGGTGAGACCCTTGAGGAGAGGGAGGCTGGTTCAACCATGG
                     atctaat  putative branch site (score: 3)
                              ttttactcttctgctt  putative PPT
        aatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaccaaccaattatttagctgttccctgtcttcggcatagccactgccattcaatgaatgttcacatctaatggttttactcttctgcttggatgccagTTTGTTGGAGACAAGGTTGCTTTTGCTCTGTCTCAGGGACTAAAGGTCATTGCATGTGTTGGTGAGACCCTTGAGGAGAGGGAGGCTGGTTCAACCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
-caccaac
- - - - - - - - - gctgttc
- - - - - - - - - - - - - - - - - - - - - - - gccattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - atgaatg