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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaaaatcttgcattgatccattccaatccgaggtcacctgaattagtcatatgactatatcagtaatttatttcattctcgttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA

Basic information

species Zea mays
transcript GRMZM2G155962_T03
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155962_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g32150.1 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------gtaaaaaaaatcttg--cattgatccattccaatccgaggtcacctgaattagtcatatgactatatcagt---aatttatttcattctcgttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA
                                                  |||||| ||  |     || |     || |  |   | || |    |  ||   | |  |  |  |  ||   ||||| ||   ||    ||| || ||| ||||||||||||||||||||||| ||| |||||||||||||||| ||||||||||| ||||| |  || |||||||||||||||||||| |||||||||
gtaaatgtttcttgaatccatctgatctgaaactcatatggttttatcgataaaaagaagttcaattataggattctttctctgatatgttaatgcacataccaacacaataaactaggttataatttgttgattttgtttttgttgtagCGTGTTGAAGAAATACCCATCCAAATTCATTGGTTGCTGTCTTGCTAATCCTGCAGATGATGGAAGCGGCATTAAACAGCTTGAACATCTAATTGTACAA

upper sequence: GRMZM2G155962_T03 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G10680.1 (Glycine max), 3'ss of exon 5
gtaaaaaaaatcttgcattgatccattccaatccgaggtcacctgaatta--gtcatatgactatatcagtaatttatttcatt--ctcgtttttt--atagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA
   |    | | | |   | |    |||||      |||    | ||||    |  | | | |||||   | |||  |    |    |||||| ||  | ||  | ||||||||||||||  |||| || |||||||| |||||| | ||||| ||||| ||||| | |||| |||| ||| ||||| ||||  || |  | 
--gagttcactatagtcatcacatcttccatgaatgggttcttttaatttttatagtgttattatatggtttattactcatgtcaattcgtttattggacagCATTTTGAAGAAATACCCGACCAAATTTGTTGGTTGTTGTCTTACTAATCCAGCAGATGATGGAAGTGGGCTTAAGCAGTTTGAAGATCTTGTTTTGAAG

upper sequence: GRMZM2G155962_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT2G35450.1 (Arabidopsis thaliana), 3'ss of exon 3
-gtaaaaaaaatcttgcattgat---ccattccaatccgaggtcacctgaattagtcatatgactatatcagtaatttatttcattctcgttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA
   |  |||| | ||  | ||||   ||| || | || |   |  |    |||      | |    | |     ||   |||     |  || || | |||||  |||||| ||||||||| ||||| || ||||| || ||||| ||||||||||| ||||| | ||| ||||  || |||||  ||||  || || | 
gaaattaaaagttttcaagtgattctccaatcaagtctgcaatatcagcgatttaattcaagttacttttgaagatgatttttgagtttcttattgacagTGTTCTGAAGAGATACCCATCAAAGTTTGTCGGTTGTTGCCTTGCTAATCCTGCAGAAGATGGCAGTGGAATTACGCACCTTGAGAATCTTGTTTTAGAG

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|93284051|gb|EB676315.1|EB676315
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|60397566|gb|DN230382.1|DN230382
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322966|gb|FL249424.1|FL249424
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|20507977|gb|BQ279847.1|BQ279847
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322963|gb|FL249421.1|FL249421
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|21987683|gb|BQ779211.1|BQ779211
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322962|gb|FL249420.1|FL249420
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|76909087|gb|DV163216.1|DV163216
EST:     TCATTCGTTGGTAACTAG                         TG-GGTGAAGAAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATC
genomic: TCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAG-AAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATC
EST: gi|101390398|gb|EB817133.1|EB817133
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322965|gb|FL249423.1|FL249423
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322967|gb|FL249425.1|FL249425
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAA                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322961|gb|FL249419.1|FL249419
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|26456812|gb|CA828395.1|CA828395
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211322964|gb|FL249422.1|FL249422
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|78090807|gb|DV519181.1|DV519181
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|26558292|gb|CA830527.1|CA830527
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211320799|gb|FL249416.1|FL249416
EST:     GTTATTGTTCAACCTGTTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|76909089|gb|DV163217.1|DV163217
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|60357568|gb|DN224541.1|DN224541
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211320798|gb|FL249415.1|FL249415
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211320801|gb|FL249418.1|FL249418
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
EST: gi|211320800|gb|FL249417.1|FL249417
EST:     GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAG                         TGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC
genomic: GTTATTGTTCAACCTATTAATCATATGTTTGATCATTCGTTGGTAACTAGgtaaaaaaaa ... ttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgaattagtcatatgactatatcagtaatttatttcattctcgttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA
                              tttatttcattctcgt  CT-rich tract
                           taatttatttcattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaaaatcttgcattgatccattccaatccgaggtcacctgaattagtcatatgactatatcagtaatttatttcattctcgttttttatagTGTGTTGAAGAAATACCCATCCAAGTTCGTTGGTTGCTGTCTTGCGAATCCTGCAGACGATGGGACTGGGATTAAACAGCTTGAACATCTGATTGTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG