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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaaccttcatttgcttactcataattatactttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag

Basic information

species Zea mays
transcript GRMZM2G171060_T02
intron # 6
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 6
lower sequence: LOC_Os02g49980.2 (Oryza sativa), 5'ss of exon 5
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctca--accttcatt--------tgcttactcataatta--tactttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag
||||||| ||||| ||||| ||||||||||| || || ||||||||||||||||||||||||||||||||  |||| ||||| || |||||||||||||||| || | |  |||||   |        |  | |  | | | |   || || ||| ||||| | ||| || |||                              
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaag------------------------------

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g49980.1 (Oryza sativa), 5'ss of exon 5
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctca--accttcatt-tgcttactcataattat---------actttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag
||||||| ||||| ||||| ||||||||||| || || ||||||||||||||||||||||||||||||||  |||| ||||| || |||||||||||||||| || | |  |||||   | ||    ||  | ||  |         | || ||| ||||| | ||| || |||   |||  |||| |   |||  |       
TGCTGACAAAACAATCTTTAGCTGGGATTCCTTTACTAGTCCTTGGCAACAAAATTGACAAGTCAGAAGCTGTTTCAAAGCAAGCGTTGGTTGATCAACTgtgagtttactaccttttctgtgtgagcttgtcatccttgagtggctaattactgaatgatgtttcaactgaagtggtct-ttctcatgtatttcag-------

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA14G39540.1 (Glycine max), 5'ss of exon 5
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctc----aaccttcatttgcttac-tcataattatactttctgcatgatatctcagctcaa-gctctctgctctcttccctttttgttttcag
|  |||| ||||  ||||||  ||||||||| |||||||| ||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||| |||| || ||    || |   |||  ||||  ||||  |  |  |||    ||   |  |   ||  | ||| | || | |  ||| |   || ||||||
TATTGACAAAACCTTCTTTGAGTGGGATTCCTTTGCTTGTTCTTGGAAACAAAATTGACAAGTCAGAAGCTCTTTCTAAGCAAGCATTGGTAGATCAGCTgtgagttctagaaatcaatattgccttatatcatcttcttttttttattattgaaatttgtcttgatgctttatgattttctccttgggtgatttcag

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA02G41170.1 (Glycine max), 5'ss of exon 5
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa--------------ccttcatttgcttactc----ataattatactttc----tgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag
|  |||| ||||  ||||||  || |||||| |||||||| ||||| ||||||||||||||||||||||| ||||| ||||| || ||||| ||||| |||| || || |              | |  || |  || ||     | ||  | | | ||    ||  | || |  |   |  | |  |  | | |  ||| |  ||| ||||||
TATTGACAAAACCTTCTTTGAGTGCGATTCCTTTGCTTGTTCTTGGAAACAAAATTGACAAGTCAGAAGCTCTTTCTAAGCAAGCATTGGTAGATCAGCTgtgagttctagatatcaatattgtcttatatcttttttctttaaaaaaaaaaaattgtcctgatgtgttatgtaactaattgaacatttggattttctccttggttgatttcag

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
lower sequence: AT5G37680.1 (Arabidopsis thaliana), 5'ss of exon 4
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaaccttcatttgcttactcataattatactttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag
|||| ||||||| ||||||   ||| |||||  | ||  | |||||||||||||| || ||||| ||||| || || ||||| || ||||||||||||||||||| |     ||||   |   |  || ||  || ||   | |  | ||| | |  |     | | |     |                  
TGCTAACGAAACCGTCTTTAAATGGCATTCCTCTTCTGATTCTTGGCAACAAAATCGATAAGTCTGAAGCTCTCTCTAAGCAAGCTTTGGTTGATCAACTgtaagtttcttattcaaa-gtccatacaaaacaat-ctggattcgag-tatatgactttggattgttttgatgcag----------------

upper sequence: GRMZM2G171060_T02 (Zea mays), 5'ss of exon 6
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 5'ss of exon 6
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaaccttcatttgcttactcataattatactttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag-----------------------------------
|  |||| ||||  || ||| |||| ||||| || |||||  |||||||||||||||||| ||| ||||| |||||| ||||  | ||||| | |||||||| || |||            ||    ||||    | |||    ||  ||| |   ||| |   |    || | ||    |||||| ||  |                                   
TCTTGACAAAACCATCCTTGACTGGAATTCCTTTACTTGTTGTTGGCAACAAAATTGACAGGTCGGAAGCTCTTTCGGAGCAATCGTTGGTGGGTCAACTgtgagttcagaaccagacgagttttcaataaaatcatttttgatatactattt-gcctcgatggcaaacctttttttatattttgtgttttgacatattttttttcctccttggtggtggttttcag

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|16927627|gb|BM080696.1|BM080696
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|76286949|gb|DV026517.1|DV026517
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|113702664|gb|EE680168.1|EE680168
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|211076142|gb|FL255312.1|FL255312
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGAC
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGAC
EST: gi|34391306|gb|CF384534.1|CF384534
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|32806604|gb|CD958838.1|CD958838
EST:     AAAATTGACAAGTCAGAAGCGCCTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|76286861|gb|DV026429.1|DV026429
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|28566462|gb|CB278110.1|CB278110
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGA-GCAGGCCTNGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCCACATGATCTCG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCG
EST: gi|149077255|gb|EE165928.2|EE165928
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|8103003|gb|AW927671.1|AW927671
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGTGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|32809543|gb|CD961777.1|CD961777
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|40287223|gb|CK327615.1|CK327615
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|78086343|gb|DV514736.1|DV514736
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|78113799|gb|DV532188.1|DV532188
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|211078882|gb|FL255321.1|FL255321
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAAT-GATAAAGGACCCGGGAGGTTTGTTGCTACATGATCTNCG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACC-GGGAGGTTTGTTGCTACATGATCT-CG
EST: gi|78086342|gb|DV514735.1|DV514735
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|148953854|gb|EC899230.2|EC899230
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|78113800|gb|DV532189.1|DV532189
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|32919725|gb|CF024537.1|CF024537
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|110945770|gb|EE165927.1|EE165927
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|89760881|gb|DY689115.1|DY689115
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|12046965|gb|BF729104.1|BF729104
EST:     AAAATTGGCAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGTGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|38229789|gb|CF920102.1|CF920102
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
EST: gi|32793765|gb|CD946001.1|CD946001
EST:     AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCACCT                         TGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG
genomic: AAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaa ... ttgttttcagTGGACTGGAATTGATAAAGGACCGGGAGGTTTGTTGCTACATGATCTCGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGACGAAACAGTCTTTGGCTGGGATTCCCTTGCTTGTCCTTGGCAACAAAATTGACAAGTCAGAAGCGCTTTCGAAGCAGGCCTTGGTTGATCAACTgtaagctcaaccttcatttgcttactcataattatactttctgcatgatatctcagctcaagctctctgctctcttccctttttgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC