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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaacttaagatgcattaccatgcttgattggtgttttgattctaatccatggctgctgtgcttcgcag

Basic information

species Zea mays
transcript GRMZM2G171060_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 2
CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaa-cttaagatgcattaccatgcttgattggtgttt--tgattctaatccatggctgctgtgcttcgcag
||||||||||||||| || |||||||||||||| |||||  |||||||||||||||| || || || || ||||| ||||||||||| |||| || ||  || ||| |  |   |||||||  |    |  ||  |  || || |||| | | ||||   |||||| |||
CTTGTTTTTCAAGCAGGAGATGGAGCTCTCCCTGGTTGGCCTGCAGAATGCTGGGAAAACATCACTAGTTAATGCTGTTGCTgtatgtatcatctaacggaatctttatttatcttaccattttaatgttatgcctggtggttttaattcgttgctggcatgcttctcag

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 5'ss of exon 2
CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaa---cttaagatgc--attaccatgcttga------ttggtgttttg-attctaatccatggctgctgtg--cttcgcag-
|||||||||||| ||||| |||||||| || ||||||||  | || |||||||||||||| || || ||||||||| |||||||  | |  || |   |||     || ||  |   | ||  || || ||       |  | ||  |  ||  | | | ||  | || ||   ||  ||  
CTTGTTTTTCAAACAAGAGATGGAGCTGTCACTCGTTGGACTTCAAAATGCTGGGAAGACTTCTCTTGTCAATGCCATTGCTgtgagtagaaatttcatcagaggttttagtcgataaatagtattctcgaacaaatctaatcttacgcgtttcacttcttgttttctttggatttgtcaag

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 3
lower sequence: EFJ11035 (Selaginella moellendorffii), 5'ss of exon 2
CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaacttaagatgcattaccatgcttgattggtgttttgattctaatccatggctgctgtgcttcgcag
 ||||| |||| |||||||||||||||||| ||  ||||  | || || ||||| |||||||||||||| ||||   |||| ||||| |  || || |  |     |||        | | ||||  || | ||||    ||  ||||| || |             
TTTGTTCTTCACGCAAGAAATGGAGCTCTCGCTGATTGGACTCCAAAACGCTGGCAAGACGTCGCTGGTGAATGTGATTGCGgtatggaa-aattcgcgaatgcgcagaga----gtctttcttggctgatcttttctagctcctccattgcag-------------

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|211076135|gb|FL255305.1|FL255305
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076134|gb|FL255304.1|FL255304
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAG
EST: gi|211078875|gb|FL255314.1|FL255314
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACTTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076132|gb|FL255302.1|FL255302
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|76286949|gb|DV026517.1|DV026517
EST:     CTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: CTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076136|gb|FL255306.1|FL255306
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076137|gb|FL255307.1|FL255307
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076142|gb|FL255312.1|FL255312
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|34391306|gb|CF384534.1|CF384534
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211078883|gb|FL255322.1|FL255322
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076141|gb|FL255311.1|FL255311
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076129|gb|FL255299.1|FL255299
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|76286861|gb|DV026429.1|DV026429
EST:     CTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: CTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|28566462|gb|CB278110.1|CB278110
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|149077255|gb|EE165928.2|EE165928
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076140|gb|FL255310.1|FL255310
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211078880|gb|FL255319.1|FL255319
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|40287223|gb|CK327615.1|CK327615
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|78086343|gb|DV514736.1|DV514736
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|78113799|gb|DV532188.1|DV532188
EST:     TCGTTGGGGTGCAGAATGCTGGGAAGACGTCGCGGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211078879|gb|FL255318.1|FL255318
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211078882|gb|FL255321.1|FL255321
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|78086342|gb|DV514735.1|DV514735
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|148953854|gb|EC899230.2|EC899230
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|78113800|gb|DV532189.1|DV532189
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|85152988|gb|DW587926.1|DW587926
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTCGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076139|gb|FL255309.1|FL255309
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|110945770|gb|EE165927.1|EE165927
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211078874|gb|FL255313.1|FL255313
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|89760881|gb|DY689115.1|DY689115
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|38229789|gb|CF920102.1|CF920102
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCT                         ACAGGTGGCTACAGTGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG
EST: gi|211076133|gb|FL255303.1|FL255303
EST:     TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCTGTTGCT                         ACAGGTGGCTACAGCGAGGACATGATTCCAACG
genomic: TCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatca ... tgcttcgcagACAGGTGGCTACAGTGAGGACATGATTCCAACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTTTTCAAGCAAGAAATGGAGCTCTCCCTCGTTGGGTTGCAGAATGCTGGGAAGACGTCGCTGGTCAATGCCGTTGCTgtatgcatcaactcactcaacttaagatgcattaccatgcttgattggtgttttgattctaatccatggctgctgtgcttcgcag

- - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA