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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTACGCTGAGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgttaacatttccgtccttagttttccttcaagtacactttggttttcattaaaatggcaatttaattggttatgggtaggaaactagctgctcaaaaaccactgatgatttttcttttcctcaaacaatttggaccaaccttatcgtcctttttaatattgattctgcag

Basic information

species Zea mays
transcript GRMZM2G120517_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G120517_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os04g35520.3 (Oryza sativa), 5'ss of exon 10
TGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTACGCTGAGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgttaacatttccgtccttagttttcctt-caagtacactttggttttcattaaaatggcaatttaattggttatgggtaggaaactagctgctcaaaaaccactgatgatttttcttttcctcaaacaatttg-gaccaaccttatcgtcctttttaatattgattctgcag----------------------------------
||| || ||||| |||||||||||||| |||||||| | |||||| || |  |||||||||||||||||| |  |||||||||| ||| | || ||  |||| |||| |||||| |  |||||||||||||||| | |  ||||     | || |   |   ||| |   | || || |  | |||     || | |   | |||||||||   | || | ||| || |  |  | | | | |||| | ||  |||| |  |  |  || |   |||                                   
TGCAGAAAAATACGCAGAGGACCAAGAAGCATTCTTTAAAGACTATGCCGGAGCTCATGCTAAACTGAGCAATCTGGGTGCAAAATTCAATCCTCCTGAGgtgagtgataacatctt-gtccttagttttcctttccacaacacgccactcttgaccgactgggccac--agttagt-agagatagt---ttatccg---acaaaccactgccaagttgtttttacccccgatgactagcgcccaatccta--gtccgtggtccttctgttgtggcaaactgagagtatgtgactgtttggttgtcctgcag
















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|4887369|gb|AI677468.1|AI677468
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|166654842|gb|EG143147.1|EG143147
EST:     TGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: TGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|7162396|gb|AW520018.1|AW520018
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|60342201|gb|DN209174.1|DN209174
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|24934386|gb|CA452604.1|CA452604
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|71327463|gb|DR800349.1|DR800349
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|67022725|gb|CO451474.1|CO451474
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|7216381|gb|AW562503.1|AW562503
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|101393103|gb|EB818482.1|EB818482
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCCCCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|60397958|gb|DN230774.1|DN230774
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|74246091|gb|DT654005.1|DT654005
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|7204636|gb|AW559169.1|AW559169
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|60349847|gb|DN216820.1|DN216820
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|5740004|gb|AI947694.1|AI947694
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCNCCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCCCCAGAACCNCAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|211351874|gb|FK984289.1|FK984289
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCGAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGSACCAGAACC
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACC
EST: gi|76920121|gb|DV168019.1|DV168019
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|76292512|gb|DV032080.1|DV032080
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|211216297|gb|FL460273.1|FL460273
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         A
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcag-
EST: gi|211216297|gb|FL460273.1|FL460273
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         A
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcag-
EST: gi|60342528|gb|DN209501.1|DN209501
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|71759931|gb|DR957868.1|DR957868
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|14244899|gb|BG842837.2|BG842837
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|88753851|gb|DY537992.1|DY537992
EST:     AGGCTCATGTTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCCCCGCAG                         GGATTTTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGCACCAGAACCACAGTCCGTGAAACA
EST: gi|7145161|gb|AW506642.1|AW506642
EST:     AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAG                         GGATTCTCTTTGGATGATTAGTGCGGC
genomic: AGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgtta ... gattctgcagGGATTCTCTTTGGATGATTAGTGCGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGAGAAATATGCAGAGGACCAAGACGCATTCTTCAGAGACTACGCTGAGGCTCATGCTAAACTGAGCGAATTGGGTGCAAAGTTCCAACCACCGCAGgttagtgttaacatttccgtccttagttttccttcaagtacactttggttttcattaaaatggcaatttaattggttatgggtaggaaactagctgctcaaaaaccactgatgatttttcttttcctcaaacaatttggaccaaccttatcgtcctttttaatattgattctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG