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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttgacatctaaattggatttaactcggccttgctgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC

Basic information

species Arabidopsis thaliana
transcript AT5G49720.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA09G02160.1 (Glycine max), 3'ss of exon 5
gtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttga--catctaaattggatttaactcggccttgc-tgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC
                                       | |  |||||  |  |   | |     | | ||||    |         || | |  ||  ||||  |||  |     | | | | |||    |||    |   |||   |    |||   ||| |||| |||||||||||| || || || || |||||  ||||||||||||||||||| |||||||| |   | ||||||| ||| || || || |||||||| ||  |||
--------------------------------------gtgtgtgatattctgctactttaag---agagatgatgtct---------atggcatcaaactcttcctaatgttatcgtatcactatgaggtgtctgggctaatttttcttttctcttctgtgtgtttttgcagATTGATTACATCCTTGGAAATAACCCAAGGAAAATGAGTTATGTCGTAGGTTTTGGTAATCATTACCCAAAACACGTCCACCATAGAGGAGCATCTGTAC

upper sequence: AT5G49720.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G40090.1 (Glycine max), 3'ss of exon 3
gtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttgacatctaaattggatttaactcggccttgctgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC
                                                                       ||  | ||||   |   ||  ||  ||      | |||   | | | | |    | | |          || |  ||| | ||||  ||  ||| | |||||||||| || || || || ||||||||||||||||| ||||| || |||||||| |   | || |||| |||||| || || ||||| || || ||||
------------------------------------------------------------------gtgggtgctagttttctgctccataataataatgatgatgtaa-tacaagtgtctgggctaata----------atctttctctgtcttg--gtgattttgtagATTGATTACATCCTTGGGAAGAACCCTCGGAAAATGAGCTATGTTGTAGGTTTTGGTAATCATTATCCAAAACATGTTCACCATAGAGGTGCGTCTATAC
















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|47830557|gb|CK120241.1|CK120241
EST:     GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAG                         ATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
genomic: GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttc ... attttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
EST: gi|124748993|gb|EH839123.1|EH839123
EST:     GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAG                         ATTGATTATATACTGGGTAAAAAACCCTCGGAAAATGAGTTATGTCGTTGG
genomic: GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttc ... attttggcagATTGATTATATACTGGGTAAAAA-CCCTCGGAAAATGAGTTATGTCGTTGG
EST: gi|116458640|gb|EG501232.1|EG501232
EST:     GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCAAGATCCCAG                         ATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
genomic: GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttc ... attttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
EST: gi|86039673|gb|DR335428.1|DR335428
EST:     CTAGATCCCAG                         ATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
genomic: CTAGATCCCAGgtattgcttc ... attttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
EST: gi|47829810|gb|CK119494.1|CK119494
EST:     GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAG                         ATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT
genomic: GACCTAATTTCTATTCGACAAGTGTGCTACGTGACTTTGCTAGATCCCAGgtattgcttc ... attttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttattttgacatctaaattggatttaactcggccttgctgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC
                         atttaac  putative branch site (score: 3)
                 taaattggatttaa  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgcttcttttcctttactctttacagaaatggtaatctcagatatagtaatggataagatccaaaaatgacacttttaaccaagattgtacgaagatctttttaaactccattttttattttgacatctaaattggatttaactcggccttgctgtattttggcagATTGATTATATACTGGGTAAAAACCCTCGGAAAATGAGTTATGTCGTTGGTTTTGGCACAAAATACCCAAGACATGTGCATCACAGAGGAGCTTCGATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT