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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattatcatttttttttgcctaaacatcattactgagttgcgaccacacagttatcaaaatctgacagcttttcttctcacttgtttattgacctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAGAGTGTATTGCGAGAAAAG

Basic information

species Arabidopsis thaliana
transcript AT5G45170.1
intron # 4
splice site 3'
intron type U2

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|125130583|gb|EL173725.1|EL173725
EST:     AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAG
genomic: AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAG
EST: gi|116478591|gb|EG521183.1|EG521183
EST:     AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
EST: gi|124928860|gb|EL006463.1|EL006463
EST:     TTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: TTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
EST: gi|125191254|gb|EL206208.1|EL206208
EST:     TTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: TTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
EST: gi|124834897|gb|EH919336.1|EH919336
EST:     GAAAAGGTGCTGCTGATGAAGNGAAAATGTTGCTTTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: GAAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
EST: gi|124880336|gb|EH959238.1|EH959238
EST:     TTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAAGTGAGAAAGCAAGTTTTGTAAA
genomic: TTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACC-AGTGAGAAAGCAAGTTTTGTAAA
EST: gi|116478590|gb|EG521182.1|EG521182
EST:     AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAG                         ATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: AAAAGGTGCTGCTGATGAAGAGAAAATGTTGCTTTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
EST: gi|124972173|gb|EL045884.1|EL045884
EST:     CTTTTGTATTTCAACCAG                         ATTGGTTGG-CTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG
genomic: CTTTTGTATTTCAACCAGgtaaattatc ... ctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttatcaaaatctgacagcttttcttctcacttgtttattgacctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAGAGTGTATTGCGAGAAAAG
                                      tattgac  putative branch site (score: 2)
                                            cctctcttc  CT-rich tract
                                 ttgtttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaattatcatttttttttgcctaaacatcattactgagttgcgaccacacagttatcaaaatctgacagcttttcttctcacttgtttattgacctctcttcagATTGGTTGGCCTTCGTCGTTGCCAACCAGTGAGAAAGCAAGTTTTGTAAAGAGTGTATTGCGAGAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG