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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttcaaagtctatagttatataattgccttgtgatttgatttacccgccttctctttgtttggttgccattgttctaacatcctttcttgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCACCATCTGGTTCAGGTTTGCCTTGAAAAAGAAATGTCTTTAGGTGACAGT

Basic information

species Arabidopsis thaliana
transcript AT5G52650.1
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|47830180|gb|CK119864.1|CK119864
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCCGCANATTACCAGCCATCTTTCCAA                         GGAAGTGNCCGTGNNTTTGNCCGTGNTGCTGNTGGCTACCGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|47830738|gb|CK120422.1|CK120422
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|164072461|gb|ES094040.1|ES094040
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTG
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTG
EST: gi|164138413|gb|ES065458.1|ES065458
EST:     GGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: GGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|86085719|gb|DR381478.1|DR381478
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGGCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|47828157|gb|CK117841.1|CK117841
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|47831024|gb|CK120708.1|CK120708
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|86075270|gb|DR371027.1|DR371027
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGGCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|86082450|gb|DR378209.1|DR378209
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGGCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|124857204|gb|EH941641.1|EH941641
EST:     AGCTCCCGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGACAGCTGC
genomic: AGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCG-CAGCTGC
EST: gi|124884994|gb|EH963896.1|EH963896
EST:     AAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: AAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
EST: gi|86081910|gb|DR377669.1|DR377669
EST:     TTGGAGGTGAAAAGGGTGGAGCTCCTGCAGATTACCAGCCATCTTTCCAA                         GGAAGTGGGCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA
genomic: TTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctc ... tgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgccttctctttgtttggttgccattgttctaacatcctttcttgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCACCATCTGGTTCAGGTTTGCCTTGAAAAAGAAATGTCTTTAGGTGACAGT
                             ttctaac  putative branch site (score: 1)
                                     tcctttcttgtttatc  CT-rich tract
                                            ttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttcaaagtctatagttatataattgccttgtgatttgatttacccgccttctctttgtttggttgccattgttctaacatcctttcttgtttatcagGGAAGTGGCCGTGGTTTTGGCCGTGGTGCTGGTGGCTACAGCGCAGCTGCACCATCTGGTTCAGGTTTGCCTTGAAAAAGAAATGTCTTTAGGTGACAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - tcaaagt
- - - - - - - - - - - - - - - - - gatttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctttct