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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgactgatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC

Basic information

species Arabidopsis thaliana
transcript AT3G55380.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g62244.3 (Oryza sativa), 3'ss of exon 1
gtgactgatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactctt--ttgactgc-agTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC
         ||| ||       |  ||   ||   |    |  | |||  |   || | |      ||| | ||  |  | ||| ||||||| | ||||||   || |||||||||||||||||||| ||||||||||||||  |||| || ||||||||   ||| |||||||| || || |||||
---gtcagctttcctcattgtaacttcatgtttctgtaactccatgatccataattttaacacagcataatattggtcaattgccagTTTATCCGGATGGACGTGTATGCATTTCTATTCTTCATCCGCCTGGTGATGATCCCAATGGTTATGAGCTTGCGAGTGAGCGTTGGACACCAGTGCATAC

upper sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G012052_T01 (Zea mays), 3'ss of exon 3
gtgactgatttttctggaaaatatatctctttctcgagcttttaggat-ttagtcttctgatgatttatactcttttgactgc--agTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC
        |     | |  |  || |||  |   | |  ||| |  ||   |   ||||||  |||  |  | |||||| | |  ||||||| ||||||||   ||||||||||||||||||||||| |||||||| |||||  |||| || ||||||||    ||||| ||||| || || || ||
-------gtaagcatcgctatcatgtcttgtctacta--tttgatcatgccaaagttctgacaattctttttgttttgaattctcagTTTATCCTGATGGACGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAATGGTTATGAGCTTGCAAGCGAACGATGGACACCAGTGCACAC

upper sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G007276_T03 (Zea mays), 3'ss of exon 3
gtgactgatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgc--agTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC
|| |       |   |||   ||    | | |         | | |  | |   ||||||  |||  || | |||||| | |  ||||||| | |||||    ||||||||||||||||||||||| |||||||| |||||   ||| || ||||||||    ||||| ||||| || || || ||
gtaagcttcactatcggactgtactcatgtctactatctgatcatg--tcaaagttctgacaattcttattattttgaattctcagTTTATCCGGATGGGCGTGTTTGCATTTCTATTCTTCATCCACCTGGTGAAGATCCCAGTGGTTATGAGCTTGCAAGCGAACGGTGGACACCAGTGCACAC

upper sequence: AT3G55380.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S75_236V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------gtgact---gatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC
               |||||    ||           |  ||  | ||  |   | | ||  |  ||| |    |    ||   |    |||    |||||||||| ||||||||   ||||||||||| ||||| ||| ||||||||||||||||  |||| || ||  | ||   ||| |||||| | || || |||||
gaaagaactctggtttgactctgaatgcactcatgtgacttaatttttctttacgatgttctg-cttatttccataccaatccttgacttttcatgtgcagTTTATCCTGATGGACGGGTTTGCATTTCAATTCTACATGCTCCTGGTGATGATCCAAATGGTTATGAATTGGCGAGTGAGCGTTGGTCTCCCGTGCATAC

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|86066037|gb|DR361794.1|DR361794
EST:     AGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATG                         TTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGG
genomic: AGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATGgtgactgatt ... ttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGG
EST: gi|86066034|gb|DR361791.1|DR361791
EST:     AGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATG                         TTTATTCTGATGGAAAAGTTTGCATTT
genomic: AGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATGgtgactgatt ... ttgactgcagTTTATTCTGATGGAAAAGTTTGCATTT
EST: gi|86066036|gb|DR361793.1|DR361793
EST:     NGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATG                         TTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGNGATG
genomic: AGTTTCACCACCAACTGTGACGTTTACCTCGGAGATGTGGCATCCTAATGgtgactgatt ... ttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC
                                           ttttgac  putative branch site (score: 3)
                                      tactctttt  CT-rich tract
                                 atttatactctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgactgatttttctggaaaatatatctctttctcgagcttttaggatttagtcttctgatgatttatactcttttgactgcagTTTATTCTGATGGAAAAGTTTGCATTTCTATTCTTCATCCTCCTGGTGATGATCCTCATGGATACGAGCTTGCCTCTGAACGTTGGACCCCTGTCCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT