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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataactaactaactaactaactaaaccaattcgaaattctgaattctcacatccttttgtttggttgcaaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT

Basic information

species Arabidopsis thaliana
transcript AT4G25700.1
intron # 1
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|47830830|gb|CK120514.1|CK120514
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
EST: gi|125204949|gb|EL219903.1|EL219903
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACAT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACAT
EST: gi|86061532|gb|DR357289.1|DR357289
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
EST: gi|124845524|gb|EH929961.1|EH929961
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCT
EST: gi|86061534|gb|DR357291.1|DR357291
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
EST: gi|125226963|gb|EL241048.1|EL241048
EST:     ACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCT
genomic: ACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCT
EST: gi|47830828|gb|CK120512.1|CK120512
EST:     CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAG                         GGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT
genomic: CTTCTATGGCTGTTATGGCTGTTTACTACAGATTCTCTTGGCAAATGGAGgtataactaa ... caaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccaattcgaaattctgaattctcacatccttttgtttggttgcaaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT
                     ttctcac  putative branch site (score: 2)
                                ttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataactaactaactaactaactaaaccaattcgaaattctgaattctcacatccttttgtttggttgcaaaaatcagGGAGGTGAGATCTCAATGTTGGAAATGTTTGGTACATTTGCTCTCTCTGTTGGTGCTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT