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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacttgtaccataagagtggcaaaaatcgttatttgcgaggtttattcggttagagatttcctgattgagtgttttctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAAACATGGAGACTTCTTGAGGCTG

Basic information

species Arabidopsis thaliana
transcript AT4G26940.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G26940.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G007185_T01 (Zea mays), 3'ss of exon 5
-gtaaaacttgtaccataagagtggc------aaaaatcgttatt-tgcgaggtttatt--cggt-tagagatttcctgattgagtgttttctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAAACATGGAGACTTCTTGAGGCTG
 ||| || || |    | |   |  |      ||| ||  || || |     ||||| |  | |   |   |  |  || | |  | |   || |   |||| ||| | | ||||||||| | |||||||| |||||||| || || |  ||||||||||||||| ||||||||
tgtacaattttttttttgactttatccactcaaaagataatttttctttttagtttactgtcagcacaagcaagtaatgctcgtctatgccctcttt-cagTGCTATTTCAGGTGGAATTGTCGATAGAGCAATTCAGGCAGAGGATAAGAAACATGGAGACTTCATGAGGCTG
















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|116483920|gb|EG526512.1|EG526512
EST:     AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAG                         TTCTACTCCCGG
genomic: AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAGgtaaaacttg ... ctgtgggcagTTCTACTCCCGG
EST: gi|116459773|gb|EG502365.1|EG502365
EST:     AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAG                         TTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAG-CTGAAGAAAGTAA
genomic: AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAGgtaaaacttg ... ctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAA
EST: gi|116459771|gb|EG502363.1|EG502363
EST:     AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAG                         TTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAA
genomic: AAGCTCGAGGAAGAGAAAGGGATCGTGATGCGGTTTGTGATAGGCCATAGgtaaaacttg ... ctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcgaggtttattcggttagagatttcctgattgagtgttttctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAAACATGGAGACTTCTTGAGGCTG
                            tcctgat  putative branch site (score: 3)
                                       tgttttct  putative PPT
          tttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacttgtaccataagagtggcaaaaatcgttatttgcgaggtttattcggttagagatttcctgattgagtgttttctgtgggcagTTCTACTCCCGGTGGAATTCTTGATAGAGCGATTCAGGCTGAAGAAAGTAAACATGGAGACTTCTTGAGGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA