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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcctctctggacaccagcaattaaaaaacaaatccagaaactactctgctttcatatatgtgcagtaatttctccagaaactactctggacaccagcttcatttcttgccatacaacctctgcttttggtatgaacatctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC

Basic information

species Zea mays
transcript GRMZM2G081188_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081188_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 10
gtatgtcct-----ctctggacaccagcaattaaaaaacaaatccagaaactactctgctttcatatatgtgcagtaatttctccagaa-actactctggacaccagct--tcatttcttgccatacaacctctgcttttggtatgaacatctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC
|||  ||||     |  ||  ||||||||  |||| | |||| ||| | |  ||  ||| ||  | | | | |      |  |  |||     | |     |||  |      || ||| | ||||  |  | |    ||  |||           |||| | ||| |||| ||||||||||||||||||||||||||  |||||||||| |||||||||||||||||||| || ||||| ||||| |||||||| ||||| |||||||
gtacatccttagttccttgaccaccagcacataaaca-caaacccacagaagacattgcattt-tctgtttcc-----ctcttaaagagtgtcatttcattcactggtcggctatatctgggcatatgaaatatttccttcatat-----------atctaacttacagGATGAGAGATACATGGTAACATATAACCCCGCAAAGGATAAGGTATATGCTTTGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCC

upper sequence: GRMZM2G081188_T03 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
gtatgtcctctctggacaccagcaattaaaaaacaaatccagaaactactctgctttcatatatgtgcagtaatttctccagaaactactctggacaccagcttcatt-tcttgccatacaacctctgcttttggtatgaacat-ctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC
                                                 |  || ||  | |  | ||   |  || | |||    | ||      |||  ||   |  | |||  |||  |    | ||| ||  |      | ||  ||  ||  | | ||   |||||||| || ||||||||||||||  ||||  | || || |||||  |||||||||| |||||||| ||||| |||||| | ||||| || ||||
------------------------------------------------gtaagcctttct-tgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
















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|74240504|gb|DT648418.1|DT648418
EST:     AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAG                         GACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
EST: gi|211302733|gb|FL372536.1|FL372536
EST:     AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGAACTCTGTTTGAG                         GACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
EST: gi|32936978|gb|CF041797.1|CF041797
EST:     GAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAG                         GACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: GAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
EST: gi|31353527|gb|CD437884.1|CD437884
EST:     AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAG                         GATGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
EST: gi|211481484|gb|FL479226.1|FL479226
EST:     TCTTGCCATACGACCTCTGTTTGAG                         GACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: TCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
EST: gi|32930803|gb|CF035615.1|CF035615
EST:     AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAG                         GACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT
genomic: AAGCATTTCAAGAGCCAGCTTCATTTCTTGCCATACGACCTCTGTTTGAGgtatgtcctc ... ttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgccatacaacctctgcttttggtatgaacatctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC
                                           tcttaat  putative branch site (score: 3)
                                         tatcttaattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcctctctggacaccagcaattaaaaaacaaatccagaaactactctgctttcatatatgtgcagtaatttctccagaaactactctggacaccagcttcatttcttgccatacaacctctgcttttggtatgaacatctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT