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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgcagttccgagtttatgttttaacttctccaattattctaatattggcag

Basic information

species Arabidopsis thaliana
transcript AT3G14100.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 2
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtg---------aatttttttagcatcgctttgtctgaaaggtgc---agttccgagtttatgtttt---aacttctccaattattctaatattggcag
 |||||||  |    ||||||||||| |||||||| |||||| | ||||| ||||| ||||||| ||||           | ||| |   |||   |   ||      |||   |||||  | ||  | ||||   ||| ||| ||   | | |    ||     
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttctaaattcttcttttaagaacatctacataaaatatggcttttc---

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G008611_T01 (Zea mays), 5'ss of exon 3
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtg---------aatttttttagcatcgctttgtctgaaaggtgc---agttccgagtttatgtttta--acttctccaattattctaatattggcag
 |||||||  |    ||||||||||| |||||||| |||||| | ||||| ||||| ||||||| ||||           | ||| |   |||   |   ||      |||   |||||| | ||  | ||| |  || ||||||   | | |    ||     
ATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGTgtaagtgttggaagttgttctttctctgatcttataccctagggactgctatagttccaaattcttctttaagaacatctccataaaatatggcttttct--

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA16G01230.1 (Glycine max), 5'ss of exon 2
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgcagttccgagtttatgttttaacttctccaattattctaatattg-gcag-----------
 | || ||  ||||||||||||| || ||||||||||||||||| ||||||||||| || |||||||||  | |    |   |   |||| ||   |     | ||        || ||||   || |   || ||| | ||  || |||            
ATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtgtttgtccagacattttttttgccttttactcctattttatctcccatttttttgtttttttcatgattgtgattgtgtgcaaaccagcttagg

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G04640.1 (Glycine max), 5'ss of exon 2
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgcagttccgagtttatgttttaacttctccaattattctaatattggcag---------------
 | || ||   ||||||||||||  | ||||||||||||||||| ||||||||||| || |||||||||  ||| | |||      ||| | ||     | |  ||   | ||||| | | |  || |    || ||  |  ||||  |                
ATTGAACCATATCCAAGTGGAAATTTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGTgtgagtg--tttgtctagacattttttttttgccttttactcttaatattttatctctca-tttttttgtttgtttcatgattgtgattgtgtgcaaacaagc

upper sequence: AT3G14100.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 5'ss of exon 2
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgca--gttccgagtttatg--ttttaacttctccaattattctaatattggcag---------
 |||||||  | ||||||||||| || ||||||||||||||| | ||||| ||||| || |||||||||  || | |   |||   ||| |||      |     ||| |  |||| |   || | |    | ||| ||    |  | |   |          
ATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGTgtgagtgt-ttgtctggacatttttttttcttttgttttttttgttgcatgtttgttgcttctcatgcatgcaactagaagagcacttttatttttcttaa

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|124821341|gb|EH906207.1|EH906207
EST:     CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGT                         GTATGTTGGAAACATCCATACACAGGTCACAG
genomic: CCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaat ... atattggcagGTATGTTGGAAACATCCATACACAGGTCACAG
EST: gi|125162320|gb|EL189090.1|EL189090
EST:     CAAGTGGAAACCTTCCTCCTGGTTTTTGATCCCAGTACTTGCCGTAGCGT                         GTATGTTGGAAACATCCATACACAGGT
genomic: CAAGTGGAAACCTTCCTCCTGGTTTT-GATCCCAGTACTTGCCGTAGCGTgtgagtgaat ... atattggcagGTATGTTGGAAACATCCATACACAGGT
EST: gi|124792955|gb|EH882634.1|EH882634
EST:     TACTTGCCGTAGCGT                         GTATGTTGGAAACATCCATACACAGGTCACAGAGCCTTTGCTTCAAGAGAT
genomic: TACTTGCCGTAGCGTgtgagtgaat ... atattggcagGTATGTTGGAAACATCCATACACAGGTCACAGAGCCTTTGCTTCAAGAGAT
EST: gi|124867827|gb|EH952264.1|EH952264
EST:     AAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAAGACGT                         GTATGTTGGAAACATCCATACACA
genomic: AAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTA-G-CGTgtgagtgaat ... atattggcagGTATGTTGGAAACATCCATACACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTAGAGCCTGTTCCAAGTGGAAACCTTCCTCCTGGTTTTGATCCCAGTACTTGCCGTAGCGTgtgagtgaatttttttagcatcgctttgtctgaaaggtgcagttccgagtttatgttttaacttctccaattattctaatattggcag

- - - - - - -  AGTGGA