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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

Basic information

species Arabidopsis thaliana
transcript AT3G46440.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag
| || ||||| || ||||| || || |||||||| || || ||  ||||||||||||| |||||||| ||||| ||||||||     |||||     | ||   | |    |||   | ||| || | |        ||| |  || ||||| ||     || |  |||    |   ||| |||||
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaa----tattttt---agttcatacct----ttttgtcttgtgatgtac-----tggattgtagttctccttaat-----aagtattttccaatctatctctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgc--------ttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag
|||||||||| ||||||||||| || |||||||| |||||||| |||||||||||||| |||| ||| ||||| ||||||||   | ||| ||   || |  ||              |||   | |||  ||| || || || |   |   || ||  |  ||| ||| | | | ||||| |  |   | | |||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagtcctctttgttatgtg-ataactctgggcttatgatttttt-ttcttaacagtgtttatcatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 5'ss of exon 9
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaac----tttctccctgtaatttgcatcaacatattctcattgtcctttattccttaa-attgtttttgtttcttctttgtag
|||||||||| ||||||||||| || |||||||| || ||||  |||||||||||||| |||||||| ||||| ||||||||   | ||| ||   || |  ||      | |        |  |||| |   ||   | |  |   |    || |  ||| || ||| | | | ||| |  |   | | |||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatcatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaac----tttctccctgtaatttgcatcaacatattctcattgtcctttattccttaa-attgtttttgtttcttctttgtag
|||||||||| ||||||||||| || |||||||| || ||||  |||||||||||||| |||||||| ||||| ||||||||   | ||| ||   || |  ||      | |        |  |||| |   ||   | |  |   |    || |  ||| || |||||   | ||| |  |   | | |||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatcatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 7
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaac----tttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag
|||||||||| ||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||||||   | ||| ||   || |  ||      | |        |  |||| |   ||   | |  |   |    || |  ||| ||  | | | | ||| |  |   | | |||||
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgattttttattaacagtatttatcatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaactt-tctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag
| || ||||||||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||||||   | ||| ||   || |  || |    | | ||  |  |||| |   |||  | |  |   |    || |  ||| | |     | | ||| |  |   | | |||||
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G157772_T01 (Zea mays), 5'ss of exon 5
GTGTT-AGGAGCTGTTATGATGAAGGCAAGCGTGTTGCT-GAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaac--tttctccctgtaatttgcatcaacatattctca--ttgtcctttattccttaa-attgtttttgtttcttctttgtag
||||| ||||| ||||||||||| || |||||||| ||  ||||| |||||||| ||||| |||||||| ||||| ||||||||   | ||| ||   || |  ||      | |     |  |  |  |  ||   || |    | |||    || |  ||| || ||||| | | ||| |  |   | | |||||
GTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatcatctatgtctgtag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagt-------tgcattttctcaggctctcgctt-caactttctccctgtaatttgcatcaaca-----tattct-cattgtcctttattcctta-----aattgtttttgtttcttctttgtag-------------
| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| |||||||| ||||| |       |  ||||| ||    ||||  |  |||| |        |     |||  ||||       || | || ||   || | |  | |     || |   | || | ||| |||  |              
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 9
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgca--ttttctcaggctctcgcttcaactttctccctgtaatttgcatc-aacata---ttctcattgtccttta-ttccttaaattgtttttgtttcttctttgtag--
| ||| | || || |||||||| || || || || |||||||| ||||||||||| ||||| ||||| |||||||||||||| ||      ||| |     | |   |||  ||   |   | |||     ||| || | |   || || ||||  ||||  ||||| |  ||||| | | || | |    |   
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCTGAGACATTGATGTTTGATTACCATAGGCAGCATGGAATTGgtaatttattgtctttttttccttataatttcttctcgttttgtttaaggcatatccaatagagatttttctttgttttttaactccttgaggtgtttatatatcctttcaacatag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA12G06980.3 (Glycine max), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaag---ttgcattttct------caggctctcgct--tcaactttctccctgtaa----tttgcatcaacatattctcattgtcctttattcctta----aattgtttttgtttcttctttgtag-
| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| || ||||| |||||    ||   ||||||      ||   ||||  |  | |     |   | |||     ||||||    | |   || ||   |  | | ||  |       || ||||  ||| || | | |   
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattccttatcttttctccttggcaacatctcattgttgagggcacaaacagtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcag

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgca-tcaacatattctcattgtc-ctttattccttaaattgtttttgtttcttctttgtag
||||  ||||||| |||||||| || |||||||| |||||||| ||||||||||| || || ||||||||||| || ||||| ||   | || |     |    | | |||   || |    ||| || | |    ||||     ||||  ||||||   ||  |  |                    
GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAGgtaacttttgtgtttttttttttaatcctgaacaaacttcaatgaatatgaagttttaatatgtatgttgtttctttatattttggacag--------------------

upper sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttat-tccttaaattgtttt-tgtttcttctttgtag
| || || ||||| ||||| || || |||||||||||||||||  | |||||||||||||| ||||| |||||  ||||||   |  |  |||     |||  | |  | ||||       |||   ||   |   | || |    ||||  | | | ||  ||  ||    | |||   | | |   
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgta---tatacattc-----ctcgtgttgtatcttttctaagttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgtaaaatatttaaacctggc--

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|47831999|gb|CK121683.1|CK121683
EST:     GCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG                         AAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCG
genomic: GCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgca ... ttctttgtagAAATCCGCATTGCTAGAATCTTCAACACTTATGGTCCACGCATGAACATCG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaagttgcattttctcaggctctcgcttcaactttctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA