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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactggctgtttcactgctttcatctgagaaaccagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG

Basic information

species Arabidopsis thaliana
transcript AT4G12590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G08370.1 (Glycine max), 3'ss of exon 2
gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactg-gctgtttcactgctttcatctgagaaac-cagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG
                                                                            |||  || | ||  | |      |||||||     | ||     |||  | |||  |||| | | | ||| |    |  | |   | |||  |||   ||         ||||||| ||||| |||||| |||| |||||||| || |||||| |||||||||| || ||| | ||||| || |||||||||||||| || ||||| || | 
---------------------------------------------------------------------------catacatgtgttgacttatgatagtcatctgcttggcacaacc--ttggattcat--tacttttactattt-acctcttgaaaatgtttaaaactttcatgc-------acaGCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAATGGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTT-

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 5
gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactggctgtttcactgctttcatctgagaaaccagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG
                                                                            ||||   ||||  | |      |||||||     |   |   |||  | ||| |   | ||  || ||||    |  | |   | | |  |||         || ||||||||| ||||| |||||| |||| |||||||| || |||||| ||||||| || || ||| | ||||| || |||||||||||||| || ||||| || ||
-------------------------------------------------------------------------cgcataaagtgctgacttatgatagtcatctgcttggc--atagcttggattcattactattta--ttatttacctcttgaaaatgttttaaactt---------tcatgcagCCAAGATACCCTTTCCATTGACACAGAGGTTTAGGTCAATGCTACAGAACGGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 3'ss of exon 4
gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactggctgtttcactgctttcatctgagaaaccagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG
                                                                           |  |  |  | || | | || ||  |||     |||      ||| |||   |||||  | | ||| | |  |  |   ||| |||| |  ||  | | ||| ||   ||||||| ||||| || ||  |||||||||||||  | || |||||||| ||||| ||||| ||||||||||| |||||||||||||| || ||||| || ||
--------------------------------------------------------------------------cttcacttttccgtataattgtttatatc-----aac------attatttttttgataggcaagtttatatcaacattattagaatctgaatctgttatttttttccc-cagCCAAGATACCTTTCCCCTTGACTCAGAGGTTTCGCTCCATGTTACAAAATGGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG

upper sequence: AT4G12590.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 4
gtttatttcctaaacaaagtgttttgcaattatttttcttggttacttcataaacagcaatcatgtatttgattttataactggctgtttcactgctttcatctgagaaaccagttaattgtttccatgatactctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG
                                                                           |  |  |  | || | | || ||  |||     |||      ||| |||    ||||  | | ||| | |  |  |   ||| |||| |  ||  | | ||| ||   ||||||| ||||| || ||  |||||||||||||  | || |||||||| ||||| ||||| ||||||||||| |||||||||||||| || ||||| || ||
--------------------------------------------------------------------------cttcacttttccgtataattgtttatatc-----aac------attattttttagataggcaagtttatatcaacattattagaatctgaatctgttatttttttccc-cagCCAAGATACCTTTCCCCTTGACTCAGAGGTTTCGCTCCATGTTACAAAATGGAATTGATTTGAGCACTGTAGATGTTAGCTATGTCAGCAGTCGCTCATG

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|164137436|gb|ES054441.1|ES054441
EST:     CTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
genomic: CTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
EST: gi|125258797|gb|EL272882.1|EL272882
EST:     TTCTCCGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
genomic: TTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
EST: gi|125285735|gb|EL299820.1|EL299820
EST:     ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATG
genomic: ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATG
EST: gi|164053653|gb|ES045035.1|ES045035
EST:     ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCAC
genomic: ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCAC
EST: gi|164053759|gb|ES144709.1|ES144709
EST:     GACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAA
genomic: GACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAA
EST: gi|124831302|gb|EH915741.1|EH915741
EST:     CACTCACTTTTGCATGGGTCAACTTCTTCTTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAAT
genomic: CACTCACTTTTGCATGGGTCAACTTCTTC-TTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAAT
EST: gi|86079343|gb|DR375100.1|DR375100
EST:     ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
genomic: ACACTCACTTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
EST: gi|164222432|gb|ES204461.1|ES204461
EST:     TTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAG                         CCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG
genomic: TTTTGCATGGGTCAACTTCTTCTTCTCTGGATTTGTTGCAGgtttatttcc ... tatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actctaatttttttataattccatagcatctaaggcttctttgtttatcttgcagCCAAAATACCATTTCCACTGACTCAGAGGTTCAGATCAATGTTACAGAATGGCATTGACTTGAGCACTGTCGATGTTAGCTATGTGAGTAGTCGTTCCTG
 ctctaat  putative branch site (score: 3)
                                   cttctttgtttatctt  putative PPT
     aatttttttataattc  TA-rich tract