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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttattttcttgctccattttccatgatttgaaccccaatcctaattcctctagcctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G06600.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 12
-------------------------------gttttattttcttgctccatt-ttccatgatttgaaccccaatcctaattcctctagc--ctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
                               ||   |||  ||   |   |  || ||  | ||   | |   |  || ||     | |  || |  | |||   ||   |      ||| | || || |  || |||||||||||||| |   | || || |||||||||||||| |||||||| ||||||||||| ||||| || || || ||||| |   
gtcgtttttactattaataactgttcattaagtgcaattcactgatttagtggttgcagcaatttccctcatcttgtatttatgtcatcatcttatttgtttctcttttggatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACA---CCCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATTCGTGAGAGCGACAAGGATA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os11g36470.1 (Oryza sativa), 3'ss of exon 8
----gttttattttcttgctccattttccatgat--------ttgaacccca-atcctaattcctctagcctgacatatttgctttcgtgt---cttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
    ||| ||  |  |   |  || ||  |||||        ||||||  || ||  |  ||   ||        |  |||  | || | |   ||   ||| | || || |  |||||||||||||| ||     |||| || |||||||||||||| || ||||| ||||||||||| || ||||| || ||||| || |   
gtgtgttctacctgataattg-atattgaatgatatgagatattgaactacatatgtttgttttcctgtttccgtaattttaatctcttttgggctgaacagTTGCCTCAAATAAATCCTGGTTTCAACAACG---CTCCATTTAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTACATCCGTGAGAGTGATAAGGACA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 2
gttttattttcttgctccattttccatgatttgaaccccaatcctaattcctctagcctgacatat-ttgctttcgtgtctttt-cagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
||   ||| | |    | | | | |||    |  |   |   |  | ||    || | |  |   | || |||   ||| |    ||| | || || |  || |||||||||||||| |   | || || |||||||||||||| |||||||| ||||||||||| ||||| || || ||||||||||   
gtaacattctttatgacaaatgttcattcaatacaatacttgcggacttgtattaactttcctcttatttcttctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACA---CGCCATTTAAATTCACAAAGTATTCGAATGCCTACATGCTTGTCTATATACGTGAGAGTGACAAAGAGA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G071441_T02 (Zea mays), 3'ss of exon 8
gttttattttcttgctccattttccatgatttgaaccccaatcctaattcctctagcctga-catatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
                   |  | ||||      || | || | |  |||   |||| ||   | ||    |||    |  || ||||| || || || || ||||| ||  ||| |    | ||  | | ||| || ||| | || ||||||||||||||||| || || ||||||||||||||||   
------------------gtaatacatg---cagacactaaacttc-ttcaattagcttgggtacataacatttatctttgttgcagCTCCCGCATACCAACCCTGGGTTGGATACTG---CACCGCTTAGATTTACCAAGCATTCAAATGCTTACATGCTTGTTTACATTCGAGAAAGTGACAAAGATA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 12
---------gttttattttcttgctccatt---ttccatgatttgaaccccaatcctaattcctctagcctgacatatttgctttcgtgtctttt---cagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
          || ||     |   || ||    | |  | | ||||   |   |   ||||   |     |  | ||  |  | |  | | | |    ||| | || || |  || |||||||||||||| |   | || ||||||||||||||||| || ||||| ||||||||||| ||||| || || | |||||| |   
gtaaaattctttataacaattcattcaatacaatacagttacttgaggacttgtataaattttccacttattgcttaactcttattctttgtatggaacagTTGCCTCAAATAAACCCTGGTTTCAATAACA---CACCATTCAAATTCACAAAGTATTCAAATGCCTACATGCTTGTCTATATACGTGAGAATGACAAGGATA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 12
gttttattttcttgctccattttccatgatttg--aaccccaatcctaattcctctagc-ctgacatatttgctttcgtgtctttt-------cagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
     || |  || |     ||||  |  |  |  |||   | || |   |  |   |  ||||  |  || | |||   |  ||        ||| | |||||||| || ||||| ||||| || |   |||| || |||||||| || ||||| ||||| ||||||||||| ||||| || ||||||||||| |   
---gcatgtctttaccagtgtttctttactccgtcaactttattcttgggtaattgtgtactgatctggttaccttctcctgcttgtatgaaacagTTGCCACAGACAAACCCTGGATTCAACAACA---CTCCATTTAAATTCACGAAATACTCAAATGCATACATGCTTGTGTATATACGTGAAAGTGACAAGGAGA

upper sequence: AT5G06600.2 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: EFJ13603 (Selaginella moellendorffii), 3'ss of exon 11
gttttattttcttgctccattttccatgatttgaaccccaatcctaattcctctagcctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG---
                                | |  |   ||   |||   ||||  |     | ||  | |  | |  || ||| | |||||||| ||||| || ||   ||| ||||||||||||||||| || |||||||| ||||| |||||||||||||||||| |||| || || || |   
--------------------------------gtaagcatgtc---attaaactagtttcggtgacttattgt--ttttcttacagTTGCCACAGACCAATCCCGGATT---TAACAACCCTCCTTTCAAATTTACGAAGTACTCCAATGCATACATGCTTGTATATATCAGAGAGAGCGATAAGGACA

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|125135656|gb|EL175858.1|EL175858
EST:     AGCAATATGGTGGTGAAGAAGAG                         CTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACA
genomic: AGCAATATGGTGGTGAAGAAGAGgttttatttt ... gtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaccccaatcctaattcctctagcctgacatatttgctttcgtgtcttttcagCTACCACAGACTAATCCTGGTTTCAATAATAACCCTCCTTTCAAATTCACAAAGTACTCGAATGCTTACATGCTTGTATATATCCGAGAAAGTGACAAAG
                                      ctttcgtgtcttttc  CT-rich tract
                             acatattt  TA-rich tract