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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattctgacgaagcctatttaatatttggagcaatcagctatagcatgacaatgacacaagattatgcttatttgtagccatcacttccaggcat...

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 3
GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattctgacgaagcctatttaatatttggagcaatcagctata-gcatgacaatgacacaagattatgcttatttgtagccatcacttcca-ggcat
||||||||||    || || ||| |||| ||||| || ||||| ||||| ||||| ||||||||||||||| |||| |||||||| ||||||||||||  | |  |  || | ||||||     ||| |    | |  || |  |      |||  |   | || |   | |||  | |  |||  |||| 
GTAATTCTGGCAATCTCCCTGCATTGTTACCTGATCAAGTCCGGAAGCTGAAGCAACTCAGCGTGCTAACTTTGGCTGAGTCAACCAAGgtgcaaatttaggctgatactgtctaatatgctatgcatttttttttttgcttatcctgtgtacataaagttactaag--ggagcgtttagatccttggcaa
















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|13178371|gb|BG349629.1|BG349629
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211178527|gb|FK980685.1|FK980685
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGAACGTTTCAAATGTAAG
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGA-CGTTTCAAATGTAAG
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211178524|gb|FK980682.1|FK980682
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211180924|gb|FK980686.1|FK980686
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|86472725|gb|DY239095.1|DY239095
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211180926|gb|FK980688.1|FK980688
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|78081417|gb|DV509829.1|DV509829
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|78112152|gb|DV530548.1|DV530548
EST:     TCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|149089443|gb|EE178684.2|EE178684
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|5268890|gb|AI770854.1|AI770854
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211180929|gb|FK980691.1|FK980691
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|211178518|gb|FK980676.1|FK980676
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGT
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGT
EST: gi|29129753|gb|CB380457.1|CB380457
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|71427327|gb|DR808377.1|DR808377
EST:     CAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: CAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|31352916|gb|CD437273.1|CD437273
EST:     AAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: AAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|50339563|gb|CO534689.1|CO534689
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAG                         ATACTACCGTATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA
genomic: TCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattc ... ctttcttcagATACTACCATATGATCAGCTCATGCAAGAGTTAGACGTTTCAAATGTAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAATTCTGGATTCCTTCCAGCACTGTTGCCTGACCAGGTCCGAAAGCTAAAGCAGCTCAGCGTGCTAACTCTGGCAGAGTCAACTAAGgtgcaaattctgacgaagcctatttaatatttggagcaatcagctatagcatgacaatgacacaagattatgcttatttgtagccatcacttccaggcat

- - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA