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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagtccaatggccgttcttgttttatgagtttaggatggctgatgcatgatcatcctactttgtactgttttaagatttttgagagttacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACAATGAAGACCATATCCACAAAACATGGAGTCTCTATACCAACAGTGGCTG

Basic information

species Arabidopsis thaliana
transcript AT2G27680.1
intron # 7
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|125058796|gb|EL127473.1|EL127473
EST:     TACTCCATCTCTCCAAAAATAACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC
genomic: TACTCCATCTCTCCAAAAAT-ACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC
EST: gi|124754685|gb|EH844815.1|EH844815
EST:     CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
genomic: CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
EST: gi|164095727|gb|ES135311.1|ES135311
EST:     TCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
genomic: TCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
EST: gi|124754675|gb|EH844805.1|EH844805
EST:     CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCG
genomic: CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCG
EST: gi|125230143|gb|EL244228.1|EL244228
EST:     GAATACTCCATCTCTCCAAAAATAACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC
genomic: GAATACTCCATCTCTCCAAAAAT-ACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC
EST: gi|125311354|gb|EL325439.1|EL325439
EST:     TTTTGTCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTA
genomic: TTTTG-CTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTA
EST: gi|125027714|gb|EL099983.1|EL099983
EST:     CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTG
genomic: CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTG
EST: gi|86075241|gb|DR370998.1|DR370998
EST:     CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
genomic: CTTTTGCTGGCCCTCGCTTGAATACTCCATCTCTCCAAAAATACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACA
EST: gi|125066919|gb|EL133615.1|EL133615
EST:     AAAATAACAAAAGG                         ATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC
genomic: AAAAT-ACAAAAGGgtaagagtcc ... tacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatgatcatcctactttgtactgttttaagatttttgagagttacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACAATGAAGACCATATCCACAAAACATGGAGTCTCTATACCAACAGTGGCTG
 ggctgat  putative branch site (score: 4)
                        tgttttaagattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagagtccaatggccgttcttgttttatgagtttaggatggctgatgcatgatcatcctactttgtactgttttaagatttttgagagttacattacagATGGTTGATGCATGGGGAGGGTGGAATCTATTTCAAGGTTTACTTCGAACAATGAAGACCATATCCACAAAACATGGAGTCTCTATACCAACAGTGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA