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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtatagatactgaatctacaagccagctcagatatttgtttctttctccaattttaaaaagggatctactggcatttttgcttatccatcttgct...

Basic information

species Zea mays
transcript GRMZM2G376074_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G376074_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g09270.1 (Oryza sativa), 5'ss of exon 3
GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtatagatactgaatctacaagccagctcagatatttgtttct-ttctccaattttaaaaagggatctactggcatttttgcttatccatcttgct-
||||||| |||| |||| ||| || ||||| ||||||||||||||||||||||| ||| |||| |||||||||||||||||||||||||||||||||||||||||  |  ||  ||||| | | ||      |     |     |  | || |  | || |    |   |  || |             |   |    ||  
GCGTTCCCGGAGAACAACCTCAGGAAATTCGATCAGTTTGAAAGTCTCTGGTTCTACAACCGTATATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatgagacgga--ctgaaaccataaatttttttttgcaagaactgttattgtttacttgttgcgattcagataataaagagaccataaaagaaataagcct

upper sequence: GRMZM2G376074_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA04G07850.2 (Glycine max), 5'ss of exon 13
GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgta----tggtatagatactgaatctacaagccagctcagat-atttgtttctttctccaattttaaaaagggatctactggcatttttgcttatccatcttgct
 |||||| | | | | |    |||||||||||| ||| | ||||| |||| ||| |||||  | |||||| ||||| | |||||||||||||| || ||||||    | || ||  |  |     |  |    |  |||| | |  ||||          |  |   |||   ||  | | ||      | ||  | | |     
ACGTTCCCGCAAGTCTAAAAATGGGAATTCAATTAGTCTAAAAGTTTCTGCTTCAACATCTTTATATCAGCTGAAAATGATGATATGGGAATCCTTTGGGgtaagtctagtctatgttgtatgcatgtactttaattcagtttaaatgttgtaagtaagcacatgttaaaaatattaaatagctaaggagtttccctaac-----

upper sequence: GRMZM2G376074_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv04s0008g03170.t01 (Vitis vinifera), 5'ss of exon 11
GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggta-------tagatactgaatctacaagccagct----cagatatttgtttctttctccaattttaaaaaggg--atctactggcatttttgctta-tccatcttgct-------------
||| ||  | | |||||  | ||| ||||| || | | ||||||| ||||| ||||||||  |||| ||||| ||| | |||||||||||||| || |||||| | ||       || | ||  ||   |  |    | |    || |      ||| ||| |  || | ||     |   || |      ||||||| ||  || |    | |             
GCGCTCTCGAAAGACAAATTTTGGAAATTCGATAAATCTGAAAGTTTCTGGGTCCACATCAATCTACCAGTTAAAAATGATGATATGGGAATCCTTTGGGgtaggctacatcttttaaaaaccaaacacatgattttggtttatcaaagtcacatttttttttttaaatctatgtttgataatttgtgcttatttttgttttctctaatgagttagtatatatgcag

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|67025740|gb|CO454489.1|CO454489
EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
EST: gi|60345273|gb|DN212246.1|DN212246
EST:     CATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: CATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
EST: gi|211478836|gb|FL266343.1|FL266343
EST:     GTTCTACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
EST: gi|67022296|gb|CO451045.1|CO451045
EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTNAGGA-AATCANAAGCTTCACAA-GGAA-TGTTGAGATTGA-GGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
EST: gi|76284352|gb|DV023920.1|DV023920
EST:     GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGG                         ATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT
genomic: GTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtata ... ctacatttagATCGTTAAGGAGAATCAGAAGCTTCACAAAGGAAATGTTGAGATTGAAGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTTCCAGGAGGACAAGCTCTGGGAATTCAATCAGTTTGAAAGTCTCTGGTTCCACATCCGTCTATCAGTTGAAACTCATGATATGGGAATCTTTAGGGgtatggtatagatactgaatctacaagccagctcagatatttgtttctttctccaattttaaaaagggatctactggcatttttgcttatccatcttgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaagg