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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG

Basic information

species Arabidopsis thaliana
transcript AT1G57870.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 3'ss of exon 9
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggtttttta-attgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                                 | | |||||| | || |     ||      | | |   ||     | |  | |        |||| ||  | | |  | | |||||||||||||||| ||||||||||| |||||||| ||||||||||| |||||||| || || ||||| ||||| || ||  ||||||| |||||||||
------------------------------------------------------------------------------------------------gtaacatttttct-atgatgtcctaaactgttctctcctgtgaccattgatcttgacaataacatgtttagtcatagcgccttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G138676_T02 (Zea mays), 3'ss of exon 9
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccat-ttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                             | ||  | |  |  |    ||   |   | | | ||    ||| |  || | ||||| |  | |||   |  |  |       || |  | |  ||   | |||||||||||||||| ||||||||||| |||||||| |||||||| |||||||| || || || || || || || || ||| ||||||| |||||||||
----------------------------------------------------------------------------gtgattttcttacggtatccatatgaccatatctctactgttttgctgccttcttttgcaccatgacatattgaggc-------atagcatctgcat---cttgcagGTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA16G00400.1 (Glycine max), 3'ss of exon 8
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttacc-accatttttgtagtagga-ctcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                             | |   || |  | | ||| | ||  || |  ||||||  |||    || |||||   | | |   |  | ||| |  |  |  |  | |||||| ||      ||||||||||| || ||||| ||||||||||| || |||||||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||||||
-----------------------------------------------------------------------------ttaggtttaccaagttctg-tcattgttctgatataaagttttgtagactattttcccaatggagtcatgaacaattacaatctaatgatttttattt------cagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCATGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G28730.2 (Glycine max), 3'ss of exon 9
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttac----caccatttttgtagtagga-ctcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                  ||||  ||    |  | ||  || |  ||||||  |||      ||| ||| |   | | |   |  | ||| |  |  |  |  | ||||||  |      ||||||||||| || ||||| ||||||||||| || |||||||| ||||| || || |||||||| ||||| ||||||||||||||||| |||||||||
---------------------------------------------------------------------------------ggttttccaagttttgtcattgttctaatataaagttttgtagttcactattctcccaatggagtcatgaacaattacaatctaatgatttttatct------cagGTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 3'ss of exon 8
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaacttta--ccaccatttttgt--agtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                     |   ||| ||  ||| |   |||||  ||| ||  |  |   |||||      |   | |  |  | | |     | |||| | ||| |||||   ||||||| ||||| ||||| || ||||||||||| ||||| ||||||||||||||||| ||||||||||| || || ||||| |||||||| |||||||||
------------------------------------------------------------------------------------atgctacttctatttacagaatttttg-aaagctcaaatctgtcatttaaacccaaaggaagcctcagaataagattccatg-tgtttaaattgctgtgcagGTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagct--ggcactgactaat---agtttctcactgctgattatattttttttataaaactttaccaccatttttgtagt-aggactc---------gtacattctctcttcatggttttttaattgtca-tgc-agGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
||||  |   |  |   |  | ||   |   |    |  | |||  || | ||| |     | | | |  ||   || |   |   | | |     ||| | | | |  || |   |   ||||   |    |  |  |||| | ||||          | | ||       | |||| |  ||   ||| | ||  |||| ||||| ||||| ||| | |||||||| || ||||||||||| |||||||| || || || |||||||| || ||  |||||||||||||||||
gtagcttacata-tggtagatgttgaggaagtgcaggggtctac--agcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgc-gttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagttt-ctcact-gctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                            |  | | | |  ||     | | ||    |||    | |  | ||  || |||| || |   | ||      |   |||  |       ||  || |     |||  || |      |  ||||| |         |||||| ||||| ||||| ||  | ||||||||||| ||||||||||| |||||||| || || || ||||| || || ||  |||| || |||||||| 
------------------------------------------gtagggcacaggcgatgcacggtgttg-tgttgaagggtggcgtacttgcttgctggttgtgactgttgcg-ggagtgttatga-------tgctgtggag--tgtatgttattgaggaaaagttttgtg--------gcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                               |  |   || |  |    | ||    ||   ||  ||  |   |||  | ||     |||  | |  | || |   | | | || || || |||   |   ||    |   |  |   |||     ||   |||||||||||| ||||| ||  | ||||||||||| ||||||||||| ||||||||||| || || ||||| || || ||  | || || |||||||| 
---------------------------------------------gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctg--ggttggcggtttggtttgtagctgtggtatcttgttcgt-gttggatgtgagtatggcgttgaccagacgtttc---cgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 9
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                                         |    ||  |   || |  |  |||||   ||     | |   | || |||||  |      ||  ||    ||||||| || ||||| || ||  | ||||| |||||||||||||||||||||||||| || ||||| || |||||||| ||| | ||||| |||||||||
--------------------------------------------------------------------------------------------------------gtacgcatgcattcttgct-cttttttttctgttttttttgcg-agtcgctcttgctcaagacttgcttt---tgcagGTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 9
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtag-gactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                                         |    ||  |   || |   | ||||| |  | | || |||  | | |||    | || ||||           |||||| || ||||| || ||  ||||||| |||||||||||||||||||||||||| || ||||| || |||||||| ||| | ||||| |||||||||
--------------------------------------------------------------------------------------------------------gtacgcatgcattcttgctctcttttttctttttgcgagtcgctcttgctcaagacttgctttt-----------gcagGTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAG

upper sequence: AT1G57870.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
gtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                                                                                                     |    |    ||||||   || |     |     |||     ||    ||  | |||    ||||||| | || || || ||  | ||||||||||| || |||||||| |||||||| ||||| || || ||||| || ||  | |||||||||||||||
-------------------------------------------------------------------------------------------------------------------gttggctcgttgtttttgccttatggtggctgggcgctc-----ataaagttggacttg---cgcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|116422944|gb|EG465536.1|EG465536
EST:     CTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAG                         GTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTAC
genomic: CTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttt ... tgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTACACAGAATTTAAATTTCCTCAGATAAAACCTCATCCTTGGCACAAG
                                      ttttaat  putative branch site (score: 3)
                                    ttttttaattgtcat  TA-rich tract