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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaattgtaatcttttttgaaatag

Basic information

species Arabidopsis thaliana
transcript AT3G26340.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os06g06030.1 (Oryza sativa), 5'ss of exon 4
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaattgtaatcttttttgaaatag
|||| || | || |||||||||||| | || ||||| || || || || ||||| |||||||| ||  |||| ||||||||||||||||||||||| |  || | | |   |  ||  ||  |          |||  ||    ||||  ||||| |    |    | |  | || |  | || ||  |||  ||| | | ||  |||
CTCTATTGCTGGTGCTTCAAAGCTTTTGGCCAACATCCTGTACTCCTACCGTGGGATGGGACTGTCAATTGGTACAATGATTGCTGGATGGGATGAGAAGgtgaattc---agcctacatgcc----------tttgattagaagtcttaagttt-atgtgctgt-gtgctactcta--tacttaa--tgtgttctatctcgatctag

upper sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G102596_T02 (Zea mays), 5'ss of exon 4
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaatt--gtaat--cttttttgaaatag
|||| || | || ||||| || ||  | |||||||| || |||||||||||||| |||||||| ||  |||| |||||||| |||||||||||||| |  || | |    |    |   |||   | || | ||||   |||  ||     | |  |  ||  |  ||     |     |  | || ||   | ||   | | ||||  |||
CTCTATTGCTGGTGCTTCCAAACTGTTGGCTAACATCCTTTATTCATATCGTGGGATGGGACTGTCGATTGGTACAATGATCGCTGGATGGGATGAGAAGgtgactcgtttgttttggttattacacct-tcatttttctctaagttgcatgatctatgcataatggctttcttttcttttttgaactttaatgattgttctcttgatctag

upper sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA06G17960.1 (Glycine max), 5'ss of exon 5
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaattgtaatcttttttgaaatag
 || ||  ||||||| |||||||| ||||| || ||  | || || ||||||||||||||  | |||||||| || |||||||||||||||||||| || || | | | | | ||    |||   | |   | ||||       |||   | | | ||| ||   |||     ||    |  ||                        
TTCAGTGACAGGAGCCTCAAAGCTACTTGCCAATATTTTATACTCTTATCGTGGAATGGGGTTATCTGTTGGTACCATGATTGCTGGATGGGATGAGACGgt-aattcacaagacaaattattg-agcaactttttctcagctagtcca-attgttacttac---agcatttatctcttttttag-----------------------

upper sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA04G37030.3 (Glycine max), 5'ss of exon 5
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaattgtaatcttttttgaaatag
 || ||  ||||||| |||||||| ||||| || ||  | || || ||||||||||||||  | |||||||| || |||||||| ||||||||||| || || | | | |  |||    || |  |||   | ||||       |||      ||    ||   || |     |  ||                              
TTCAGTGACAGGAGCCTCAAAGCTACTTGCCAATATTTTATACTCTTATCGTGGAATGGGTTTATCTGTTGGTACCATGATTGCCGGATGGGATGAGACGgt-aattcacacaacaaagta-ctgaacaactttttctcagctagtccaattcttacaacatttaatctcttttttag------------------------------

upper sequence: AT3G26340.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv01s0010g02900.t01 (Vitis vinifera), 5'ss of exon 5
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaat-tgtaatcttttttgaaatag
 || ||| |||| |||||||| || || || ||||| || ||||| || ||||||||||| || |||||||| || ||||||||||| ||||||||||| || |      | |  |||  ||  ||     |  |   ||  |  ||| || |||||    |  || |    ||| |  |  |    | ||||                
TTCAGTTACAGGGGCTTCAAAACTGCTGGCAAACATTCTATATTCTTACCGTGGAATGGGTCTATCTGTTGGGACCATGATTGCTGGGTGGGATGAAACGgtaa------tgagatttgaatattatgaaatgatcttttgcctatct-taatttcatgatcttaatct---gtctactttgtggggtatgtag---------------

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|164215816|gb|ES025007.1|ES025007
EST:     GTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACA                         GGCCCTGGATTGTACTATGTTGATAACGAAGGAGGACGGCTTAAGGGAGAC
genomic: GTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccc ... tttgaaatagGGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC
EST: gi|164207502|gb|ES091221.1|ES091221
EST:     AATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACA                         GGCCCTGGATTGTACTATGTTGATAACGAAGGAGGACGGCTTAAGGGAGAC
genomic: AATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccc ... tttgaaatagGGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC
EST: gi|86083116|gb|DR378875.1|DR378875
EST:     GTGGAAT-GGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACA                         GGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC
genomic: GTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccc ... tttgaaatagGGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC
EST: gi|86076876|gb|DR372633.1|DR372633
EST:     GTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACA                         GGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC
genomic: GTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccc ... tttgaaatagGGCCCTGGATTGTACTATGTTGACAACGAAGGAGGACGGCTTAAGGGAGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGTTTCAGGAGCTTCAAAGCTTCTTGCTAACATGCTCTATTCATATCGTGGAATGGGACTTTCTGTTGGCACAATGATTGCTGGATGGGATGAAACAgtcagtaccctaaactttatatcctaactgttatttccttctcggtctgtagtttcactcaccaaagcgaaagtcgagatgctaaaattgtaatcttttttgaaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA