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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttacttactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag

Basic information

species Arabidopsis thaliana
transcript AT2G34560.2
intron # 9
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os01g55260.2 (Oryza sativa), 5'ss of exon 8
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttact-tactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag---------------
|||||| ||    || ||||| ||  | ||||||||  | |||||||||||| | || |||||||| || |||||||||||||| || || |||||||| |||   ||||  |  | ||   ||  | |         |||         |    | | ||   ||    |     |  |||| |               
GGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAACGGgtacattttttttacattccggtactatagtccaataagtaggggcgggattaaatttgtaaatcttctttgtaatagtcatttgagctttgccttggat

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G115766_T02 (Zea mays), 5'ss of exon 8
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctttt--acttactctcatagaacaaaaat-gcttgtatcatgattttcttttgtttaggcctcaactagtg-aaaccattag------------
|||||||||    || ||  ||||||| || |||||| |||||||||||||| | || |||||| | |||||||| ||||| || || || ||||| || ||||||||||  |  || |||  |    ||||  |   |||  | |  | |||| |   | | |      |   ||  | ||   ||             
GGATGGGTTGACTAAGACAGATGAGCTTGTTTTTGTTCTAGCAGCAACAAATTTACCATGGGAATTGGATGCAGCAATGCTGCGTCGGCTGGAGAAGCGTgtatccttttctaaataatcttgtgtttcaaatcttagttgatttacaaatttcatgcatattgttagagatatgtatagacttgtatatctttgtactc

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA08G09050.1 (Glycine max), 5'ss of exon 9
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctt-------------ttacttactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag------
|||||| ||    || ||  |||| || || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |||||||||||             || |||| |    |  |  | |||||  ||  |||   |||    |  | ||    |||  |        |||| |      
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGCGAgtatccttcaaatataagcttttgcttagtagtgtgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttact---tcattggcctgga

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA05G26100.1 (Glycine max), 5'ss of exon 9
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttt---tacttactctcatagaacaaaaatgcttgtatcatgatt---ttcttttgtttaggcctcaactagtgaaaccattag-----------
|||||| ||    || ||  |||| || || |||||||| || ||||||||||| ||||||||| | |||||||| |||||||| ||||| ||||| || ||||||||    ||    || |   | |  |    ||| ||    |||| |   |    || | ||| |||| |   || |    | |             
GGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTGGCGGCAACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGACGTCTTGAGAAGCGTgtatccttcaaatataagcttttgcatagtagtg-tgcatgataaatgaatgggtcaaattttctagtcctctaaatgtcattttacttcattggcctgga

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 5'ss of exon 9
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttacttactctcatagaacaaaaatgcttgtatcat----gattttcttttgtttaggcctcaactagtgaaaccattag------------
|||||| ||    || ||  ||||||| || |||||||||||||||||||||||||| |||||| | |||||||| |||||||| || || || ||  ||||||||||||  |   ||  ||   ||     | |   |  |||     | ||||| |     ||  ||    || |  |   || ||            
GGATGGTTTGACAAAGACAGATGAGCTTGTTTTTGTTTTAGCAGCAACAAATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGAgtatccttttgatgggtcaaatcatactttgtttcagatggcatttttaactttctgtcagaaagttctagtttactatatatatgagagagagagagag

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ34591 (Selaginella moellendorffii), 5'ss of exon 5
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttactta-ctctcatagaacaaaaatgcttgtatcatgattttcttttg--tttaggcctcaactagtgaaaccattag
|||||| ||   | || | || || || || || || || ||||| |||||  |||| ||||||||||| || || |||||||||||||| |||||||| ||    ||  |   | || ||||    | | | || || |  |  ||| |      |  ||   | ||    | | | |||      
GGATGGCTTGATGCAAGCCAACGATCTGGTGTTCGTCTTGGCAGCCACAAACATCCCATGGGAACTAGACGCGGCCATGCTCCGGCGTCTCGAGAAACGCgtgagtttgcaaagatctttcatg---ccagagtggttcttcctggatctgagaaagacttcgtggcttgtttggagcaacag----

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: EFJ09429 (Selaginella moellendorffii), 5'ss of exon 5
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttactta-ctctcatagaacaaaaatgcttgtatcatgattttcttttg--tttaggcctcaactagtgaaaccattag
|||||| ||   | || | || || || || || || || ||||| |||||  |||| ||||||||||| || || |||||||||||||| |||||||| ||    ||  |   | || ||||    | | | || || |  |  ||| |      |  |||  | ||    | | | |||      
GGATGGCTTGATGCAAGCCAACGATCTGGTGTTCGTCTTGGCAGCCACAAACATCCCATGGGAACTAGACGCGGCAATGCTCCGGCGTCTCGAGAAACGCgtgagtttgcaaagatctttcatg---ccagagtggttcttcctggatctgagaaaggctttgtggcttgtttggagcaacag----

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|47831791|gb|CK121475.1|CK121475
EST:     ATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGA                         ATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG
genomic: ATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctttt ... aaaccattagATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG
EST: gi|124781826|gb|EH871769.1|EH871769
EST:     TCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAAGAAACGA                         ATTCTTGTACCTTTACCGGAT
genomic: TCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGA-GAAACGAgtatcctttt ... aaaccattagATTCTTGTACCTTTACCGGAT
EST: gi|164097082|gb|EL984851.1|EL984851
EST:     TGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGA                         ATTCTTGTACCTTTAC
genomic: TGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctttt ... aaaccattagATTCTTGTACCTTTAC
EST: gi|86084400|gb|DR380159.1|DR380159
EST:     ATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGA                         ATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG
genomic: ATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctttt ... aaaccattagATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG
EST: gi|125267983|gb|EL282068.1|EL282068
EST:     ATGCAGCTATGCTCCGGCGTCTAGAGAAACGA                         ATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG
genomic: ATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatcctttt ... aaaccattagATTCTTGTACCTTTACCGGATCCAGAAGCAAGAAGAGGAATGTTCGAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAACGAgtatccttttacttactctcatagaacaaaaatgcttgtatcatgattttcttttgtttaggcctcaactagtgaaaccattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT