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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccagagcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG

Basic information

species Arabidopsis thaliana
transcript AT4G36280.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os10g10190.1 (Oryza sativa), 3'ss of exon 5
gtaattgttttacttagtta-atatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtc-tctaaccagagcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
       ||||   || |||  || |  ||| |    | || ||   |           | | ||  |    ||| | ||||  |  |    |  |||  ||         |||||||||||| || |||||||| || ||||||||||| |||||||| || || |||| |||| | |  |||||| |
-------ttttttctaattatgtaggcacttta---tgcttttatgtgaaaaac---aattttttaatcaatgactgttggttattcattttgcacttttctccacaacacagATGGAAATGGCTTTAAGACAAGCACGATGAGACTTGGTGCTGATGCAATAGTGTTTACTCGCGCAAACCGTGGAAG

upper sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G021864_T01 (Zea mays), 3'ss of exon 5
-gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccagagcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
  ||||| ||||| |||||   ||   |||| |  |  |  |  ||       ||||| | |    || ||       |  | ||| |||      | | | |  ||   |||||||||||| || |||||||| || ||||||||||| || ||||| || ||||||| |||  | |  || |||||
tataatt-ttttatttagtatctagcttcttta--taatagcatgtataaaactcttggtattgctgtctcttgt---tactttcttacc------ttcttctactgcgcagATGGAAATGGCTTTAAGACAAGCACAATGAGACTTGGTGCAGATGCAATTGTTTTTACTCGTGCTATCCGAGGAGG

upper sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G24450.1 (Glycine max), 3'ss of exon 4
gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccag--agcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
         ||      | ||||  || |    ||| | |||       ||   || || | |    |  |   |  |  || ||  |||   | | ||   |||   | ||||||| ||||| |||||||| |||||||||||||| || ||||||| ||| ||||| |||||  | |  | |  |||
---------ttttcagatcaataaaatttctctctc-tctctctctctctgaaatttctctttc---tctcagaaattcttcactttccaagtaacatcatgttttattctagATGGCAATGGATTCAAGACTAGTACCATGAGACTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG

upper sequence: AT4G36280.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G05800.1 (Glycine max), 3'ss of exon 6
gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccag--agcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
           ||       |  |||  || | |   |||  ||     |    || || | |   | || || |  |  || ||  |||   | | ||   |||   | ||||||| ||||||||||| || |||||||||||| | || ||||||| ||| ||||| |||||  | |  | |  |||
----------aacagtacataagtgacttttatcatattttcagattaataaaatttctctttc--tctctga-aattcttcactttccaagtaacatcatgttttattctagATGGCAATGGTTTCAAAACTAGTACCATGAGATTGGGTGCTGATGTTATTGTTTTCAGTCGGGCAATGCATTCAGG

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|19875617|gb|AU236448.1|AU236448
EST:     CATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACAACGATTGGACAGT                         ATGGAAATGGTTTCAAGACAAGT-CCATGAGACTTGGAGCTGATGCTNTCG
genomic: CATGAGCTTAGGCTACTCATCAAAGAAGTCTAATACAACGATTGGACAGTgtaattgttt ... ttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtcttggtttccgacaggtggtctctaaccagagcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG
                         ctctaac  putative branch site (score: 2)
                                     cttcccttttgtgttt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttttacttagttaatatgatcttgagctcgtttctagtcgggtggtcttgctgtcttggtttccgacaggtggtctctaaccagagcttcccttttgtgtttagATGGAAATGGTTTCAAGACAAGTACCATGAGACTTGGAGCTGATGCTATCGTTTTTAGTCGCTCCACTCGTGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG