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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttttgtattttggattgaacataatagtggaatctgtggtcattttctgacactatgaaactatgtattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGACAGCCTCAACGAGGAATCATACAAAGACAGCACTCTTATTATGCAGCTA

Basic information

species Arabidopsis thaliana
transcript AT1G22300.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0001g05720.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------gtttgtttttgtatt-ttggattgaacataatagt----ggaatctgtggtcattttctgacactatgaa-----------------actatgtattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGACAGCCTCAACGAGGAATCATACAAAGACAGCACTCTTATTATGCAGCTA
                                      | ||  |||||| || ||  ||  |  |     ||     |  | |     || |||||     | | ||                 | | ||| ||| |||| || |||||  | || || ||||| || ||||| || ||||| |||||||| ||||| || || ||||||||||| || || || |||||||||||||| 
gttgatcatgctctctgatttggactatttatttttttggtttcttttgtgttcttacatcaagaacggaggtctagaggtttttcctccactttcttgagttgttaaggttctgttttgttttaaatttgtgttgcacagGGCTTGCCACCTTGCAAAACAAGCTTTTGATGAGGCTATTGCAGAACTTGATAGCCTGAATGAAGAATCATACAAGGATAGTACCCTTATTATGCAGCTT

upper sequence: AT1G22300.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S201_25V6.1 (Physcomitrella patens), 3'ss of exon 4
gtttgtttttgtattttggattgaacataatagtggaatctgtggtcatttt--------------ctgacactatga--aactatgtattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGACAGCCTCAACGAGGAATCATACAAAGACAGCACTCTTATTATGCAGCTA
||  | ||||| | ||  | ||    ||    |||| |  ||   |  ||||              |||||  |  ||   |||  ||  ||   || |||||||| ||||| |||||||||||||| || |||||||| ||| | ||||   | |  ||||| || ||||| ||||||||  | || ||||| |||
gtaagattttg-agttgaggttttggatgcctgtgggacgtgcttttcttttggcggggttcgtaactgactgtgcgattgactgcgtggtg-gtagGGCATGCCATTTGGCGAAGCAAGCATTCGACGAGGCAATTGCCGAATTGGACACATTGAGTGAGGAGTCGTACAAGGACAGCACATTGATCATGCAACTA
















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|124785947|gb|EH875626.1|EH875626
EST:     TGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
genomic: TGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
EST: gi|125326103|gb|EL340183.1|EL340183
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGA
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGA
EST: gi|124726043|gb|EH817445.1|EH817445
EST:     ACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAA
genomic: ACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAA
EST: gi|124883384|gb|EH962286.1|EH962286
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGG
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGG
EST: gi|125313719|gb|EL327804.1|EL327804
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCA
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCA
EST: gi|125114828|gb|EL165079.1|EL165079
EST:     TGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTG
genomic: TGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTG
EST: gi|47830317|gb|CK120001.1|CK120001
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
EST: gi|125293074|gb|EL307159.1|EL307159
EST:     AGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
genomic: AGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
EST: gi|125306409|gb|EL320494.1|EL320494
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGACCAATTGGCTAAGCAAGCATTCGAT
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATG-CCAATTGGCTAAGCAAGCATTCGAT
EST: gi|47831981|gb|CK121665.1|CK121665
EST:     GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
genomic: GCGTTGAACTTTTCAGTTTTCTACTATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
EST: gi|124735359|gb|EH826761.1|EH826761
EST:     TATGAGATCTTGAACTCTCCCGAAAG                         CGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA
genomic: TATGAGATCTTGAACTCTCCCGAAAGgtttgttttt ... tattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatagtggaatctgtggtcattttctgacactatgaaactatgtattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGACAGCCTCAACGAGGAATCATACAAAGACAGCACTCTTATTATGCAGCTA
                        ttctgac  putative branch site (score: 2)
                                         tatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttttgtattttggattgaacataatagtggaatctgtggtcattttctgacactatgaaactatgtattgtacagCGCATGCCAATTGGCTAAGCAAGCATTCGATGATGCAATTGCTGAACTTGACAGCCTCAACGAGGAATCATACAAAGACAGCACTCTTATTATGCAGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT