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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G27720.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g15310.1 (Oryza sativa), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatctt----gttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                     ||   ||||    || |  |     || || | |   | |   | |        |||   |         |||||| |||    ||  | ||||  |||||||||||||||||||| || ||||| ||||| ||||| |||||||| || || || |||||||||||||| || || || || || || || ||||||
------------------------------------gtaagagaagatccgccgcttcgcgctgtgcgtggtggttg---tttggtttggtttctgatcggctagggtttgaaacttttgtgtggtttttttttagCTCGTGGAGCTTAAGAACGGCGAGACGTACAACGGGCACTTGGTGAACTGCGACACGTGGATGAACATCCACCTCCGGGAGGTTATTTGCACCTCAAAG

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G038606_T03 (Zea mays), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG-
    ||||       |       ||    || |  | |    |  ||      | || | | |   | ||         |||||  |  | | |   | || ||    ||||| ||  || || | |   ||||||||||||| |||||||| ||||||||||| |||||| |||| ||||| || || |||||||||||||||||  | || || || || || |||||| 
----gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttt-tggcgtctgattctccgttc-------aatctattgttagtcc---tgaccgttgaattgaaact-attgtgatct--cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAGG

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G038606_T02 (Zea mays), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
    ||||       |       ||    || |  | |    |  ||      | || | | |   | ||         |||||  |  | | |   | || ||    ||||| ||  || || | |   ||||||||||||| |||||||| ||||||||||| |||||| |||| ||||| || || |||||||||||||||||  | || || || || || ||||||
----gtaaggacgtaaggtcccgttggccttcttctttcgtcgtcgtttt-tggcgtctgattctccgttc-------aatctattgttagtcc---tgaccgttgaattgaaact-attgtgatct--cagCTCGTGGAGCTGAAGAATGGTGAGACATACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCATCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G095114_T01 (Zea mays), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaatt-ttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
    |||| ||  ||     ||  | |  |  | ||  | | ||  |||    |||  |||   |  || |  |||    |||   ||          | || ||     | || ||| || |||| |   ||||||||||||| |||||||| ||||| ||||| |||||| |||| ||||| || || |||||||||||||| ||  | || || || || || ||||||
----gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtg----tga--ttattcgttcagtctattgtttatcctgag-------tcctgaccgt-----taaaactttttgtgttct--cagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATTGCGACACGTGGATGAACATCCACCTTAGGGAGGTTATTTGCACCTCAAAG

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G095114_T02 (Zea mays), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaatt-ttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
    |||| ||  ||     ||  | |  |  | ||  | | ||  |||    |||  |||   |  || |  |||    |||   ||          | || ||     | || ||| || |||| |   ||||||||||||| |||||||| ||||| ||||| |||||| |||| ||||                                                  
----gtaagatcccggtgtctggcttctttcgtcgtcgtttttggcgtg----tga--ttattcgttcagtctattgtttatcctgag-------tcctgaccgt-----taaaactttttgtgttct--cagCTCGTGGAGCTGAAGAATGGTGAGACGTACAACGGGCATCTGGTCAATT--------------------------------------------------

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G37170.2 (Glycine max), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaac-ttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                               | | || | |||   |   | |  | ||     |||||   |   ||  | | |  || ||  |||   |  |  || | |   || | ||||| || || ||||| |||||||| || ||||||||||| ||||| || || |||||||||||||||||||| |||||||| |||||||| || 
-----------------------------------------------gcaactcacttttcattctcttctcttttatt-tctaacttattattattatgatggtgatggtgatgttgatgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGACACATGGATGAACATCCATCTGCGAGAAGTCATTTGTACATCTAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G39780.1 (Glycine max), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaac-ttccttttactgtaattt-----tgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                             || |  |    ||| | |    |||   || |   |||||   |   ||  | ||||| | || |     ||    | ||  || | |   || | ||||| || || ||||| |||||||| || ||||||||||| ||||| ||||| ||||||||||||||||| || |||||||| |||||||| || 
---------------------------------------------gtaactcattttttcattctctattttctttgatttctaacttattattattattactatgatatgatgatggtgatggtgatgatgtaacagTTGGTGGAACTGAAAAATGGGGAGACATATAACGGGCATTTGGTTAATTGCGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACATCTAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G17430.1 (Glycine max), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
|||||| |||      ||||    |  | ||||    | | |    | | | | |  |||  |    |||  ||      | ||   ||||||   ||      |||  ||    ||| |||||      |||| ||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||||||||| || |||||||| ||||| || || 
gtgagtcaaacc----ccctgtgctttatttttaccctctttttttttagggttacctta--ttgttattatat-----gtgta---gaacttgtgtt------aatactg---tttgatttgt---aacagCTGGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATCCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G02380.1 (Glycine max), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
|||||| |||       | ||   |  | ||||    | | |          |  | ||| || |   ||  ||   | ||  |||  |  ||  |  | ||  | || | | |  ||   | || |   |||| ||||| || || ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||| ||||| || |||||||| ||||| || || 
gtgagttaaaccct---cttttgctttatttttaccctcttttt-------ttagggttacgttattgttatat---gtatagaaattatgttaatactgcttgatttgtaacttgtgacatattgtaacagCTAGTGGAACTGAAAAATGGGGAGACTTATAACGGGCACTTGGTTAATTGTGATACATGGATGAACATTCATCTCCGAGAAGTCATTTGTACCTCTAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0060g02240.t01 (Vitis vinifera), 3'ss of exon 2
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctg--agtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattt-tgaatc-ttgtt-ttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                    | ||||    |    ||   | |||         || |  | | ||  |         |  |  || | || |||   | || ||||| || || ||| || | |||||||| || ||||| || || |||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || || ||||| 
------------------------------------acatatagcataggtctattattttcctcttcttttcctctggtgagatggctaggtattttagta-tatattttacaagtcattgttattattgtggcagTTGGTGGAGCTGAAAAATGGGGAAACTTACAATGGTCATTTAGTGAATTGTGATACATGGATGAACATCCATCTGCGTGAAGTCATCTGCACTTCAAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv07s0005g00230.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagttt--aagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                      | |||||   |||| |||  |  | || |   || | ||| |  |    |      | | |   |||||| ||  | |  |  | |||| || ||| | ||||||||||| |||||||| || ||||||||||||||||| || |||||||||||||||||||| ||||| || ||||| || ||||| ||||| 
----------------------------------cctcagatgaaaacaagcagagcctcgatgtaaaattttctttaagagttagcatctcacttcgtgacctgtaacttatactgcttgtatgttgtgatagTTGGTGGAGCTTAAAAATGGAGAAACTTACAATGGGCATTTGGTTAACTGTGATACTTGGATGAACATTCATCTTCGGGAAGTTATCTGTACCTCAAAA

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S36_327V6.2 (Physcomitrella patens), 3'ss of exon 1
---------------------------------------gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaa--gtgagcatt---------gcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
                                        |  | || ||   ||     ||| | |||||      ||  || | |  | || |    |  || | ||||         ||||   |||||   |      || |||   | |||  |   | || ||      |  | |||| || ||||| || ||||||||||| || || || ||||| || || |||||||| ||||||||||| || || |||||||| || || || ||||||
gtacgggtcacctttgccataacacttcttgaatatattctttggaacatcatgagaaaagat-agaatttcacataatgcgaggagttgttgtgcacgactgtaatcattttatatcctgcatgttggatcgttacatggatcttttaggtctaacat--gacctcgtcggtaatctgcagCTTGTCGAGCTCAAAAATGGAGAGACTTATAACGGCCATTTAGTAAACTGTGATACATGGATGAACATTCACCTACGTGAAGTTATTTGCACCTCAAAG

upper sequence: AT5G27720.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ10085 (Selaginella moellendorffii), 3'ss of exon 1
gtgagtaaaatttcgacccttgattacaattttgttatatatgaagtgaagctgagtttaagtgagcattgcattagggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG-
                                                                                     ||  |  | |||    |     ||||  |     || | || ||||||| |||||||| |||||||||||||| |||||||||||||||||||  || ||||  ||||||||||||||||| || ||||| || || || || ||| 
----------------------------------------------------------------------------------gtgagtgatgttcttcgtttccttctttgtctgaaaattcgcttgggtagCTAGTGGAGCTCAAGAATGGAGAGACTTACAATGGGCATTTGGTGAGCTGCGATAGCTGGATGAACATCCATCTACGAGAAGTTATTTGCACTTCCAAGG

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|86050911|gb|DR346666.1|DR346666
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050917|gb|DR346672.1|DR346672
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATGCAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|47831834|gb|CK121518.1|CK121518
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|47832106|gb|CK121790.1|CK121790
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|116449433|gb|EG492025.1|EG492025
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050907|gb|DR346662.1|DR346662
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050915|gb|DR346670.1|DR346670
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATGCAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050918|gb|DR346673.1|DR346673
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|116480858|gb|EG523450.1|EG523450
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATTCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050914|gb|DR346669.1|DR346669
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|116480849|gb|EG523441.1|EG523441
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGT
EST: gi|86050916|gb|DR346671.1|DR346671
EST:     CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATG                         CTCGTGGAGCTTAAGAATGGAGAGAGCATGCAATGGGCATTTGGTGAATTG
genomic: CTTCCTCTATCGCTGCTTAAAACTGCTCAAGGGCATCCTATGgtgagtaaaa ... gttttggtagCTCGTGGAGCTTAAGAATGGAGAGA-CATACAATGGGCATTTGGTGAATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggatctaaaggaacttccttttactgtaattttgaatcttgttttgttttggtagCTCGTGGAGCTTAAGAATGGAGAGACATACAATGGGCATTTGGTGAATTGTGATACTTGGATGAACATCCATCTGCGTGAAGTCATATGTACATCAAAG
  atctaaa  putative branch site (score: 3)
                                    tcttgttttgtttt  putative PPT
                  ttttactgtaatttt  TA-rich tract