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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcag

Basic information

species Arabidopsis thaliana
transcript AT4G02480.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 21
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgt----accttttattg--ctatacggattt-atttgttagtt----gttactcctacataactg-aaaccaaacatatatttga--tgtttaatgcag-
||||||||||||  |||||||||| ||||| || ||||||||| |||||||||||||||| || || || ||||||||   |||||| ||||| || |||||    || || |  ||   ||| |   | | || ||   ||      ||  ||   |  || |  |       ||  |  ||    |||||  |  || 
TGATATTGGAGCCTTGGAAAATGTAAAAGACACATTGAAGGAGCTGGTGATGCTTCCTCTGCAAAGGCCTGAATTGTTCTGCAAAGGACAGCTAACGAAGgtagagacgttatgatgaattatccatgtctcatatgcgggtgtaagattgttctatctcaattataggttgcgcacttgattagagtgttttgtcaagt

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 12
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgta-ccttttattgct------------atacggatttatt-tgttagttgtta---ctcctacataactg-aaaccaaacatatatttgatgtttaatgcag
||||||||||||  |||| ||||| || || || || |||||| |||||||||| ||| | || ||||| ||||||||   |||||| ||||| ||||||||| | |  || |||             | |  | || |||   | || ||| |    |       ||| | |     | |||||  ||||| |||       
TGATATTGGAGCCTTGGAGAATGTAAAGGACACATTAAAGGAGCTGGTGATGCTCCCTTTACAAAGACCTGAATTGTTCTGCAAAGGGCAGCTAACAAAGgtagcatcataatgcctaattatgtttgaaatcggttcattacatgaggtgtcagagttttctttcaaccgtaggttgaccatatggttgatatttttct---

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 17
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgt-accttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaat-gcag---------------
||||||||||||| | |||||||| || ||||| |||||||| || || ||||||||||||||||| || |||||||||| |||||| |||||  | ||||| |    || |   | ||    ||||  ||     ||  |    |   | | |  | |    ||| | | |      |||| | |                
TGATATTGGAGCTTTAGAAAATGTTAAGGAAACCTTGAAGGAATTAGTCATGCTTCCTCTTCAGAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCTAAGgtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattactttgggtatag

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 17
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgt---accttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaat-gcag---------------
 |||||||||||| | |||||||| || ||||| |||||||| ||||| |||||||||||||| || || |||||||||| |||||| |||||  | |||||   |  | || |   | ||    ||||  ||     ||  |  | |   ||| |  | |    |||   | |      |||| | |                
CGATATTGGAGCTTTAGAAAATGTTAAGGAAACCTTGAAGGAATTGGTCATGCTTCCTCTTCAAAGGCCTGAATTGTTTGGCAAAGGACAGCTGGCCAAGgtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatag

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 16
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgt------accttttatt--gctatacggatttatttgttagttgttactcctacataactgaaaccaaa-catatatttgatgtttaat-gcag---------------
||||||||||||| | ||||||||||| || || |||||||| ||||| ||||||||||||||||| || || ||||||  |||||| ||||| || |||||      |  || | ||  | |      | | | ||||          |  ||    |    |  | || ||| | | |      | || | |                
TGATATTGGAGCTTTAGAAAATGTGAAGGACACCTTGAAGGAATTGGTTATGCTTCCTCTTCAGAGGCCTGAGTTGTTTTGCAAAGGACAGCTGACCAAGgttgatagattttctttttagttgctttaaatgacttgtggaacacattttttagtagatcatattcgaatcatgtgtgtagcacctcattgtaattactttggatatag

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 20
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGg----taccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcag-----------------------
||||||||||||| | ||||||||||| || || |||||||| ||||| ||||||||||| ||||| || |||||||||  |||||| |||||  | ||||    ||  |||| ||  ||    | ||||  ||  |  ||  || | |   | | | | |  | |   ||||    ||| ||   |                         
TGATATTGGAGCTTTAGAAAATGTGAAGGACACCTTGAAGGAATTGGTTATGCTTCCTCTACAGAGGCCTGAATTGTTTTGCAAAGGACAGCTGGCTAAGgttggtagattttcttttta-gttgctttaaatgacaagtggaacacattttttagt-agatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatag

upper sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 20
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 20
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtaccttttattgctatacggatttatttgttagttgt-tactcctacataactgaaaccaaacatatatttgatgtttaatgcag----------------------------------------------------------------
||||||||||||| | ||||||||||| || || |||||||| |||||||||||||||||||| || || ||| | |||   || || ||||| || |||||    | | |  |       |||| ||| ||   | | ||    || |||      | |      |  |||  | |  | |   |                                                                
TGATATTGGAGCTTTAGAAAATGTGAAGGACACCTTGAAGGAATTGGTGATGCTTCCTCTTCAAAGGCCAGAACTATTTTGTAAGGGACAGCTGACTAAGgttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaatgaggttactatttttcag

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|86063354|gb|DR359111.1|DR359111
EST:     TGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAG                         CCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
genomic: TGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtacctttta ... tttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
EST: gi|124706256|gb|EH797658.1|EH797658
EST:     TTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAG                         CCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG
genomic: TTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtacctttta ... tttaatgcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATATTGGAGCTCTGGAAAATGTGAAAGAAACGTTGAAGGAGTTGGTGATGCTTCCTCTTCAGAGACCGGAATTGTTTGACAAAGGCCAGCTCACAAAGgtaccttttattgctatacggatttatttgttagttgttactcctacataactgaaaccaaacatatatttgatgtttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA