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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTGGTGACCGTGATGGGTACCGTGCAGGTCCTCGAGCTGGTGGTGAGTTTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctcactgaccataccttctatttacttctctatctcaccaacgtcatataatgtgctactcttgaagtctttatcatagagctcctgaacctg...

Basic information

species Arabidopsis thaliana
transcript AT5G52650.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G52650.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv02s0025g00310.t01 (Vitis vinifera), 5'ss of exon 4
GTTTGGTGACCGTGATGGGTACCGTGCAGGTCCTCGAG---CTGGTGGTGAGTTTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctcactgaccataccttctatttacttctctatctcaccaacgtcatataatgtgctactcttgaagtctttatcatagagctcctgaacctg---
|||||||||||| ||||||||||||| |||||| ||||   ||   ||||||||||   |||| |||||||||||||| || ||||| || || ||||||   ||||  | |||    |  |  ||   ||| | || | | |   |      | ||| |   |  |  | |        ||   || | | |  |   | |    
GTTTGGTGACCGGGATGGGTACCGTGGAGGTCCACGAGGACCTCCAGGTGAGTTTG---GTGACAAGGGTGGAGCTCCTGCTGATTATCAACCTTCTTTCAGGgtaagctatcatcttcgct--ctggcattcaattatatgttctatatgtataatagaggctaattatttctttcatcttgcaattg-gtttgttttcttaatg
















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

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTGGTGACCGTGATGGGTACCGTGCAGGTCCTCGAGCTGGTGGTGAGTTTGGAGGTGAAAAGGGTGGAGCTCCCGCAGATTACCAGCCATCTTTCCAAgtaaattctcactgaccataccttctatttacttctctatctcaccaacgtcatataatgtgctactcttgaagtctttatcatagagctcctgaacctg

- - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctatct