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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA

Basic information

species Arabidopsis thaliana
transcript AT4G21160.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 2
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
                                                          ||  ||   || |    | |    |||| | |  || | ||   ||||   |   |||  ||||   |   | ||   |  |      ||  |||||    || ||||| ||||| |||||||||||||||||||||  ||| ||| | ||| | ||||||||| ||||||||||| | ||||| ||||||||||| ||||| | | 
---------------------------------------------------------atgagttgtgtttattaagtt----aatagtgtgctgaactt---atctatttatgcttggtcttgtcgtg-cattaaaaccttgggacattattttcttacttacagGTTTTATCTGTGACATTGGATGAATGGTCAAGTGATGAAATAGATGCAATGATTGAAGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTATT

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G29940.1 (Glycine max), 3'ss of exon 2
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
                                                        | | |  || || ||| |        |||| | |  || | || ||   |    |    |||| |     | |         |   |||     |||||    || ||||| || || |||||||||||||||||||||  ||| ||| | ||| | ||||||||| ||||||||||| | ||||| ||||||||||| ||||| | | 
-----------------------------------------------------atgagttgtgtctatcaagtt--------aatagtgtgctgaacttatttatttatgcttggtcttgtcgtgcattaaagccttgggacatt----attttcttactttcagGTTTTGTCTGTGACATTGGATGAATGGTCAAGTGATGAAATAGATGCAATGATTGAAGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTATT

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 4
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggct-tacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
                                              ||| |||    ||   |||  || |||  | | ||   || |  ||   || | ||      |||  |||  ||         | |||   |         || |||||  ||| || |||| || || |||||||||||||| |||||||| || ||| | ||| | ||||| ||| |||| |||||||| ||||| ||||||||||| || || | ||
----------------------------------------------aaagtttttagtttttttc--ttcagacagttatatttatcaagtta-agagtggtgtgaatgctgaactcatt---------tgtttgatag-------cattgttttttactctc-agGTTTTGTCTGTGACATTGGATGATTGGTCAGAGGATGAAATAGATGCAATGATGGAAGTTGGGGGAAATGCTTCTGCTAATTCAATTTATGAAGCTTATA

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 4
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
                                                 ||||| | | |  ||    |   || | |||    ||  |   |     || |        | | | ||    ||  | |  ||||  ||       |  |||||  ||| || |||| || || |||||||||||||| |||||||| || ||| | ||| | ||||| ||| |||| |||||||  ||||| ||||||||||| || || | ||
-------------------------------------------------atttggcctagtttttttcttcaattggttatgtctatcaagttaagagtggtg-------cgaatgctga--actaatttgtttgacagc------actgttttttactctc-agGTGTTGTCTGTGACATTGGATGATTGGTCAGAGGATGAAATAGATGCAATGATCGAAGTTGGGGGAAATGTTTCTGCTAATTCAATTTATGAAGCTTATA

upper sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 4
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
                                                        |||   || | ||  | | | ||      ||| ||  |  |||  |   |      | || | |  | | ||| | ||  ||   ||||     ||||  ||| | ||||| || || ||| |||||||||| ||||| ||||| ||| | ||| | ||| ||||  ||||||||||| | ||||| ||||||||||| ||||| ||||
------------------------------------------------------atatttagtttctttt-gctagtttg-----aatttttagtttttcctccattttgtaaattataccaatataat-tcttaaaacaatatt----attttggactgttcagGTGTTGTCTGTGGCATTGGATGATTGGTCTGATGATGAAATTGATGCCATGGTTGAGGTTGGAGGAAATTCTTCTGCTAATTCAATTTATGAGGCTTTTA

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|125090685|gb|EL148577.1|EL148577
EST:     CTTAAAATGTTGTGGTGTCCACAGAAGCCTTGGACAGTCATATCTCAAAG                         GTCTTATCCGT
genomic: CTTAAAATGTTGTGGTGTCCACAGAAGCCTTGG-CAGTCATATCTCAAAGgttgtgactc ... aactttccagGTCTTATCCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA
       ttcttac  putative branch site (score: 2)
                                               ctttcc  putative PPT
                               tatttatagttttcaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtgactctttgcttctctttctagttttggtttatctttggtgaaaatttgccattggattccattaagatggcttacaaataatattgtggatttgttatctcgctccacttcttcttacagaatcttttgcaagtgtatttatagttttcaactttccagGTCTTATCCGTGACATTGGATGAATGGTCAGATGAAGAAGTCGATTCGATGATTGAAATTGGAGGAAATGCCTCTGCAAATTCAATTTACGAGGCGTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA