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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaacaattttcagacccagattaattattgaatgatgtcactcttagt...

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaac--aattttcagac-ccagattaattattgaatgatgtcactcttagt-------
||||||||||||||||||||| || || |||||||| || |||||||| ||||||||| |||| | ||| || ||||| || ||||||||||| ||||||||    |  | |||| |||      | || || |       |   |  |  |  |   | |||| | ||  |||||  || |||   | |  ||   |   ||       
ATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTTAGTCGCGATTATATGACTCTCAAGgt----aataccttccctt----cgtatagttacccacaaataaaaaactacttatttagttttgacacatcagat--atcattctgtaacttcttaccgcgtaacattt

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: AT1G17720.1 (Arabidopsis thaliana), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaacaattttcagacccagattaattattgaatgatgtcactcttagt----------
 |||||||| || || ||||| || ||||| |||||||| ||||| || || |||| | |||| | ||| || ||||| || ||||| ||||||||||||||  | |     |    |   | | | ||  |  || || ||||       |||| |    ||    |   | |  ||  |||    | | || |||  |          
TTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTTAGTCGCGATTACATGACGCTCAAGgttggaaatcattcggttccctttgtgtatatttttctgattgtgg----gccaatagaggtctattctttagttctttctgatatcttttaccctttttgacgtttcag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaacaattttcagacccagatt----aattattga-atgatgtcactcttagt-
 |||||||| || |||||||| || ||||| ||||||||||||||||||||||||| | |||| | | || | ||||| |||||||||||||| || |||||   |      ||||  | ||| |   | ||  |||    |||    |||   | | ||| ||    || ||     || ||| || ||| |  ||  ||  |  
TTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTTAGTCGTGATTATATGACACTTAAGgttcattaa---ttcttattttccagtgattttgtttgaagtgtt---cacatcaaagtttgcaattgcatatatggaaactatagatatgcttgcatactctgcg

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttcta--tctaattgcttttggttgtca-tgcacccaacaattttcagacccagattaattattgaatgatgtcactcttagt
| | || || || || |||||||||||||| ||||||||||| || |||||| ||||   |||    || ||||| ||  | || || ||||| ||||||||  ||   |   ||  |   | ||  | |||    |  | ||  |   || | |  |    | | | |   |||    || |  || ||   || |      
AGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTAAGTAGGGACTACATGACTCTCAAGgttagttcgaaactcgataagtgtaattgtaaaaagtgattgtcattgctggaactgaagcctgttaaaagaagaaattttgtaaaaggaaaacattggg---

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaacaat-----tttcagacccagattaattattgaatgatgtcactcttagt
|||||||||||| ||||||||||| || || || ||||||||||| |||||| | ||    ||    || ||||| || || || || ||||| || || ||  |||     |   | |  | | | | | ||      ||  ||| |    |   |||     |     | |||    |  || |||||   |  |   |||  
ATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTGAGTCGGGACTACATGACTCTGAAAgtaagtaatctttatacctagtat-tttgaatgtgggcagtgatcaagactgctgaaataaagctggtgaaaccaagagacctagtgaatagag--agcatta--

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 10
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 5'ss of exon 9
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatct-----aattgcttttggttgtcatgcacccaacaattttcagacccagattaattattgaatgatgtcactcttagt
| | || || || || ||||| |||||||| |||||||||||||| |||||| ||||   ||||   || ||||| ||  | || || ||||| ||||||||  ||   |   ||  |  |  ||  |     ||||| || |   ||    | |   ||   | |  |||    | |||| |   ||||| ||     |     
AGCTAGGTCGTTTTTCACAGAGATTATTGCTTCAATTTCTGATATCAAGTTTGCAAGAGGTGGCCGGTACATTCTGAGTAGGGACTACATGACTCTCAAGgttagtttgatactcgatattcgtaattgcgaaaattgattatcactgctg-gaattgaagcttgtctagagaatgtttaaatggagaatgttggtgaacc----

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|211384024|gb|FL015619.1|FL015619
EST:     TTTCAAGGAATGGCAAATATATTCTTAGCCGNGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCC
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCC
EST: gi|71419453|gb|DR804773.1|DR804773
EST:     TGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
genomic: TGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     TTTCAAGGGATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAG                         CTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTTCAAGTCCAT
genomic: TTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagca ... ccatactcagCTATGGGATCTAAACATGAATTCAGGCCCTGTTTCAACCTTCCAAGTCCAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTTAGCCGTGATTATATGACGCTCAAGgtgtgtagcagcttctcttgttctatctaattgcttttggttgtcatgcacccaacaattttcagacccagattaattattgaatgatgtcactcttagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA