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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaagtacatcacaaatggatcgatcatcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG

Basic information

species Arabidopsis thaliana
transcript AT1G44446.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G44446.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G11920.1 (Glycine max), 3'ss of exon 8
---------------gtaaaagtacatcac---aaatggat-cgatcatcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG
               || |  ||  || ||   ||  | || | | ||||| |     |  | ||| | || |||  |  ||| | |||    ||||   |||| |||||||| |||||||||||||| ||||| || ||||| ||||||   ||||| |||||  | |||||||| |||||  | ||||||||||| || |
ggattaacatgtagagtgagtgtgaatgactgaaagagaatactaccatctccttatttt-taacatttttattttgtgtgttgctgttgacttattaa-agGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAACGGTGCAAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGG

upper sequence: AT1G44446.3 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G42840.1 (Glycine max), 3'ss of exon 8
----------------gtaaaagtacatcac--aaatggatcgatcatcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG
                || |  ||  || ||  |||  ||    |    |      ||  | ||| | ||||||  |  ||| | |||    ||||   |||| |||||||| |||||||||||||| ||||| || ||||| ||||||   || || || ||  | |||||||| |||||  | ||||||||||| ||  
tggattaacatgtagagtcagtgtgaatgactgaaagagaatactaccgtatccttattttaacatttttgttttgtgtgttgctgttgacttattaa-agGTTTTAAACGAGGATCTACGGCTAGTGTTAGGCCAGCAAGAGCGGATGAACAATGGTGCCAATGTGTGGAATTTCCCAGTATCCTATGACAAGCTTGGGA
















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|124991112|gb|EL063381.1|EL063381
EST:     CTGTGGAGACATTTCGCTGAACAG                         GTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTA
genomic: CTGTGGAGACATTTCGCTGAACAGgtaaaagtac ... atatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTA
EST: gi|86082745|gb|DR378504.1|DR378504
EST:     TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAG                         GTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTA
genomic: TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAGgtaaaagtac ... atatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTA
EST: gi|125025720|gb|EL097989.1|EL097989
EST:     TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAG                         GTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGT
genomic: TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAGgtaaaagtac ... atatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGT
EST: gi|124741640|gb|EH832802.1|EH832802
EST:     TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAG                         GTCTTAAACGAAGAT
genomic: TAAAGAATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAGgtaaaagtac ... atatttccagGTCTTAAACGAAGAT
EST: gi|124873473|gb|EH955118.1|EH955118
EST:     AATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAG                         GTCTTAAACGAAGATCTACGGCTAAGTTTTAAGGACAACAAGAACGGATGT
genomic: AATCTTCCATTCATGGAACATCTGTGGAGACATTTCGCTGAACAGgtaaaagtac ... atatttccagGTCTTAAACGAAGATCTACGGCTA-GTTTTA-GGACAACAAGAACGGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG
                                        tttctat  CT-rich tract
                                        tttctatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaagtacatcacaaatggatcgatcatcttcaaccatcgtcacagtcttgtttcttaagttaccgtttctatatttccagGTCTTAAACGAAGATCTACGGCTAGTTTTAGGACAACAAGAACGGATGTTAAACGGAGCAAACATATGGAATTTACCAGTTGCTTATGACAAGCTCGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT