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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc...

Basic information

species Arabidopsis thaliana
transcript AT3G52560.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G071010_T01 (Zea mays), 5'ss of exon 2
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttg-agaagcatagattaatattatttgcatctcattgc-
   ||| || ||||| |||||||| ||||||||||||||||||||||  ||||||||||| ||||| || |||||||| |||||||| || |||||||| ||    | |   | |  |    ||  | | |||  || | | ||| || ||  ||||   | |    | | ||      | || || || ||   |   | | | 
AGAGAAGGGCATTGGTGATGGAACAGTGAGCTATGGAATGGATGATGCCGATGACATCTACATGCGGTCATGGACTGGTACCATCATTGGCCCTCACAATgtgagaacacaatctcatc---ctctttatatttcccgt-gcctttattta-attaaggttagacacgcacaactgccaactactagtactttgctgcaactacc

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G027378_T01 (Zea mays), 5'ss of exon 2
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttg-agaagcatagattaatattatttgcatctcattgc-
   ||| || ||||| ||||| || ||||||||||||||||||||||  ||||||||||| ||||| || |||||||| |||||||| || |||||||| ||    | |   | |     |||  ||     | ||||  | ||| || ||  ||||   | |    | | ||      | || || || |    |   |||   
AGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATCTACATGCGGTCATGGACTGGTACCATCATTGGCCCTCACAATgtgagaacacaatctc----atcctctttatctttcctgtgcctttattta-attaaggttaggcacgcacaactgccaactactagtactctgctgcaattata

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA03G35790.1 (Glycine max), 5'ss of exon 2
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgtta--tatctttttctttatctgctaacattctccttcgtcttcatatatgttaac--aattgt-tttgagaagcatagattaatattatttgcatctcattgc
    ||||| || || |||||||| || |||||||||||||||||||| || ||||| || ||||| ||||||||||| ||||| || || ||  | || |||  ||  ||||| || ||   |    |    || ||  ||   |   |  ||| |||   |  ||| ||| |   | |      ||| ||   || |||       
AGAAAAAGGAATCGGAGATGGAACAGTTAGCTATGGAATGGATGATGGTGACGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGCCCCTATAATgtaaatatttatctattactgccttgattttttttttctatcaaatatgtgcatgctaaatgagctgtattttatttgaaccagcgaatttt-catgtatc-------

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA19G38450.1 (Glycine max), 5'ss of exon 2
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc
    ||||| || || ||||| || || || ||||||||||||||||| |||||||| || ||||| ||||||||||| ||||| || |||||  | || |||  ||| | | |  |  |  ||       || | ||||   |   |  ||||||| |   | | |        |  | || |   |||| ||| |      
AGAAAAAGGAATAGGAGATGGCACAGTTAGTTATGGAATGGATGATGGTGATGACATTTACATGCGCTCTTGGACTGGAACCATTATTGGTCCCTATAATgtaaatatttatctaacactgccttgatttttttttcttcaaatatgtgcatgttaa-atgagctgtattttatttgtactagtga-attttcatgtagcaa-

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA15G21780.1 (Glycine max), 5'ss of exon 1
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc-
    ||||| ||| | ||||| ||  | ||||||| |||||||||||| |||||||| || ||||| ||| ||||||||||||| || || || || || |||   |||| | | | || |     ||  ||||  | |  ||    | | |   ||  || ||| | ||  ||||  |  |   |       |     ||   
TGAAAAAGGAATTAGAGATGGCACAATTAGCTATGTAATGGATGATGGTGATGACATTTACATGCGCTCTAGGACTGGCACCATTATTGGCCCCCAAAATgtaa--atatttctctgttcactctgtag-attcatccttatcgatgtgtgt-ccaatgatagttatcagttgcatgtaagaggctgcccccaaaaatgttaaa

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 5'ss of exon 2
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttc--tttatctgctaacattctccttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc
   ||| |||||||| ||||| |||||||| |||||||||||||||||||||||||| || ||||| |||||||| || ||||| || ||||| ||||| |||   |    |    |  |||   ||||   |   | |||  || |    ||||||  |||  |  |  |    | |  | |    |   ||  |  |      
GGAGAAGGGTATTGGAGATGGTACTGTGAGTTATGGAATGGATGATGGAGATGACATATACATGCGGTCTTGGACAGGAACCATAATTGGTCCACACAATgtaagcagccttaaaacatttttcttgctgtaacatttcttattcattcattatgttc-caaaaggatcaatcctcttccagtggggtgccttaaactttt----

upper sequence: AT3G52560.2 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 3
---GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctc-cttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc----
   |||||||||||| ||||| || || |||||||| ||||| ||||| |||||| | |  ||||| |||||||| ||||| || || || ||         ||  |  ||  || | |     ||||| |||  |  ||||  |  ||    |    | ||   ||| ||   ||   | ||  |    |     || ||       
AGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCA--------AGCCACgtcagttccgtccagagctaaaatttacatttcgcgtgaattagcgactcccatcccttttaggcacaattagtagaaaatatcaagactaataagttca

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|86062376|gb|DR358133.1|DR358133
EST:     ACATCTATATGCGTTCTTGGACTGGCACTATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86018881|gb|DR314627.1|DR314627
EST:     ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAAC---                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|86087082|gb|DR382841.1|DR382841
EST:     ACATCTATATGCGTTCTTGGACTGGCACTATCATCGGTCCTCACAACGTA                         ACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
EST: gi|164043829|gb|ES081846.1|ES081846
EST:     ACTGGCACCATCATCGGTCCTCACAACGTA                         GCTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT
genomic: ACTGGCACCATCATCGGTCCTCACAACGTAgttatatctt ... tatgtcacagACTGTTCATGAAGGTAGAATCTATCAGTTGAAGCTCTTTTGTGACAAAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGGTATTGGGGATGGAACTGTGAGCTATGGAATGGATGATGGAGATGACATCTATATGCGTTCTTGGACTGGCACCATCATCGGTCCTCACAACGTAgttatatctttttctttatctgctaacattctccttcgtcttcatatatgttaacaattgttttgagaagcatagattaatattatttgcatctcattgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctttttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaagca