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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgaataaaaaaccattgatatacctttggtgaagatggaatctgaacctcattggttaatatatatttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT

Basic information

species Arabidopsis thaliana
transcript AT2G43945.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 3
-------------------gtttgtgaataaaaaaccattgatatacctt-tggtgaagatggaatctgaacctcattggttaatatatatttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT
                    ||| |   ||       ||| ||||   || ||   |  ||   | ||  |  ||    |  ||  | |    || | |||||| || |||||||||||||| ||  | || ||||| ||||||||||||||||| |||||||| ||||| || ||||| ||||| || || ||||| || 
ggattgaaagaggagtcacatttatttttatctctgtattaatatgtattgtgactagaataccacctttatatctagtggcaac-tgttgcaatcttcagGTTATGCAATATGGACATCATCTCCAAGGTCCAACAGGTGATCTGCTTCGCGTTCCATGACAGCAAGCTGCTGATGGAAACATGCCAGGAGGCCAAGAAC

upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------------------------------------------------------------gtttgtgaataaaaaaccattgatatacctttggtgaagatggaatctgaacctcattg-gttaatatatatttatg-tgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT
                                                                                                                ||| |   |       ||||  | |  ||       | | ||  | | || || || | |    | | |    |   |||||| | ||||||||||||||||| ||||| || || ||||| || ||||| || |||||||| || |||||||| ||||| ||||| ||||| |||||||||
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT

upper sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S134_28V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------gtttgtgaataaaaa--accattgatatacctttggtgaagatggaatctgaacctc------attggttaatatatatttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT
                                                          |  | ||   | |   || ||||||||   ||   |||   || ||| ||||  |       | ||  |  |||  || | | |||||  |||| |||||||||||  || |||| || |||||||| |||||||| || |||||||| |||||| | || |||||||| |||   ||||| ||||||
gtaatgtttccagattcttggtgttttattttgtgtgtgactatgctccagtggcacatacgcgagggatatgcacgattgatattgtttacttgactttgcaatgtgaatttgtgattaactgtgtggtatg-atatgtttgcagACTGTGCAATATGGACATTGTAACACATGTGCAACAAGTTATCTGCTTTGCCTTTCATGATAGTAAGTTGCTCATGGAGACTTGTAGTGAAGCAAAAAAT

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|86087051|gb|DR382810.1|DR382810
EST:     GTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAG                         GTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATYTGCTTCGC
genomic: GTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAGgtttgtgaat ... ttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGC
EST: gi|19741914|gb|AU227267.1|AU227267
EST:     CTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAG                         GTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGC
genomic: GTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAGgtttgtgaat ... ttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGC
EST: gi|86080400|gb|DR376157.1|DR376157
EST:     GTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAG--G                         -TTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTS-TTCGC
genomic: GTGGTAGAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAGgtttgtgaat ... ttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGC
EST: gi|124997586|gb|EL069855.1|EL069855
EST:     TGGTAGTAAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAG                         GTTGTGTAATATGGACATCATAT
genomic: TGGTAG-AAAAGCCACATAATGACCATTTGCCATTGTTAGAAGCCAGCAGgtttgtgaat ... ttatgtgcagGTTGTGTAATATGGACATCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttggtgaagatggaatctgaacctcattggttaatatatatttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT
                                ggttaat  putative branch site (score: 4)
                           tcattggttaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgaataaaaaaccattgatatacctttggtgaagatggaatctgaacctcattggttaatatatatttatgtgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC