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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGGTATTAGCTTCTGATAATTACATCAAGGCTGATTCTGGCCTCATATATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttcctctatgttagattagttaaacttaggatctgaagttagatcatttatggaattggtatgctctttacttggatatatagaattgaagatatcattgagttttatggttattttgacag

Basic information

species Arabidopsis thaliana
transcript AT3G60370.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60370.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA03G26680.1 (Glycine max), 5'ss of exon 4
TAAGGTATTAGCTTCTGATAATTACATCAAGGCTGATTCTGGCCTCATATATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttcctctatgttagattagttaaacttaggatctgaa-gttagatcatttatggaattggtatgctctttacttggatatatagaattgaagatatcattgagttttatggttattttgacag
||| ||| || | || ||||| || || |||  |||||| || |||||||| || |||||    |||||||||||||||| |||||| ||||||||||||||  | |||  || || |     |  ||   ||| | |  ||||  |||  ||| |  |      |  | || || |||    ||||     | |||  ||   |                         
TAAAGTAGTATCATCAGATAACTATATAAAGAGTGATTCAGGGCTCATATACCGAGATTTTGTAGTTGGTCAAGGTGATTGCCCAAAGGATGGTCAGCAGgtttttcttt-tcaatctactgcttcttt--ctttgtaaatgaacattaagtcaatagtttggcag--aagcactctacgaaaatattagtcaatgagtattgga-------------------------

upper sequence: AT3G60370.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA07G14250.1 (Glycine max), 5'ss of exon 4
TAAGGTATTAGCTTCTGATAATTACATCAAGGCTGATTCTGGCCTCATATATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttcctctatgttagattagttaaacttaggatctgaagttagatcatttatgga--attggtatgctctttacttggatatatagaattg--aagatatcattgagttttatggttattttgacag
||| ||| || | || ||||| ||  | |||  |||||| || |||||||| || |||||    ||||||||||||||||| ||||| ||||| ||||||||     ||  |||   ||| |||   |    ||   ||||   | |   |  ||| |  |  | |  || |    ||  |||| |  |     ||   ||||||| | | |                     
TAAAGTAGTATCATCGGATAACTATGTAAAGAGTGATTCAGGGCTCATATACCGAGATTTTGTAGTTGGTCAAGGTGATTTTCCAAAGGATGGGCAGCAGgt-----tttttct---ttaaattttct----ttccaatctattgcttctttctttgtaaatgaatattaagtcaattgtttggctgaaacactttagaaagatattagtca---------------------
















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|164223413|gb|EL992912.1|EL992912
EST:     TTTCCCAAAAGATGGTCAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
genomic: TTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
EST: gi|124742130|gb|EH833292.1|EH833292
EST:     ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAG                         GTGACTCTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATA
genomic: ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATA
EST: gi|86070975|gb|DR366732.1|DR366732
EST:     ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
genomic: ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
EST: gi|125263202|gb|EL277287.1|EL277287
EST:     ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGA
genomic: ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGA
EST: gi|86070976|gb|DR366733.1|DR366733
EST:     ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGG-CAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
genomic: ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
EST: gi|125250426|gb|EL264511.1|EL264511
EST:     CAAAAGATGGTCAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
genomic: CAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
EST: gi|19875360|gb|AU236191.1|AU236191
EST:     ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAG                         GTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT
genomic: ATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttc ... attttgacagGTGACTTTTCACTACATTGGCTACAATGAGTCTGGAAGGCGAATAGATAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGGTATTAGCTTCTGATAATTACATCAAGGCTGATTCTGGCCTCATATATCGGGATTTCAATGTTGGTCAAGGTGATTTCCCAAAAGATGGTCAGCAGgtactacttcctctatgttagattagttaaacttaggatctgaagttagatcatttatggaattggtatgctctttacttggatatatagaattgaagatatcattgagttttatggttattttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG