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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT

Basic information

species Arabidopsis thaliana
transcript AT5G53170.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccact-taataata-aattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                                                 | ||   |    | ||| | |  || | ||  || | || || |    || |   | |  |||   |   |||  ||    | |  | |||    |    |||| ||||||||||||||||| ||||| ||||| ||  |||| || ||||||||||| || ||
----------------------------------------------------------------atatgccattgt-gccatctgcagctgttatcctatagtttttgtgctactgctgttgtcttgaccaaacataccttactggagctggctttttgctcc--agGCCATTGCTGGAGAAGCTGGCGTACCATTCTTTTACCGAGCAGGTTCTGAATTTGAGGAAAT

upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccact-taataata-aattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                                                |   |   |    | ||| | |  || | ||  || | || || |     | |   | |  |||   |   |||  ||   |    | || |   |     |||| ||||||||||||||||| ||||| ||||| ||  |||| || ||||||||||| || ||
----------------------------------------------------------------ggacgccattgt-gccatctccagctgttatcctatagtttttgtgctattgctgttgtcttgaccaaacatacctta--ctggagctgtctttttgccccagGCCATTGCTGGAGAAGCTGGTGTACCATTCTTTTACCGAGCAGGCTCTGAATTTGAGGAAAT

upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                                       | ||  |   |   || |       | ||    |||   | | |||   |   |   || || | || ||||  | |      |   || | | ||     |  |||||||| ||||||||||||||||| || || || |||||| |||| || ||||||||||| |||||
-------------------------------------------------------actaaaatcctacattattg-----acatcaaccttttgagttaatctattgaaatttatcattgttatgatctaata-gtgtttgctttatatgg----gaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCGTTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT

upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                                       | |   |   |   || |     ||| |          |||| ||||   |||    || || | || ||||  |    | | |   ||        |   |  |||||||| |||||||||||||| || || || || |||||| |||| || ||||||||||| |||||
-------------------------------------------------------actgaaatcctacattattgacatca-accttttgagttaatcaattgaaatt----tatcattgttatgatcta----atagtgt-ttgctttatctgggaccttgaagGCTATTGCTGGAGAAGCAGGTGTCCCATTTTTCTATCGAGCAGGCTCTGAATTTGAGGAGAT

upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                                       | |   |         | |   || ||  || || |  | |  || |||  | |         |  |||||| |  ||| |      || | | ||     |  |||||||| ||||||||||||||||| || || || |||||| | || ||||| |||||||| |||||
-------------------------------------------------------aatggaaaaacaacactactttgttattgtctacctcttgagtaaatctattgatatgtattgtgatctgatagtgtttgc------tttatatgg----gaccttgaagGCTATTGCTGGAGAAGCTGGTGTTCCATTTTTCTATCGGGCAGGATCAGAATTTGAGGAGAT

upper sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 7
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                                           |   ||||| ||  | ||        ||||||   |  | ||  | ||||| |   ||  || ||||         ||||| ||        | ||   || |  |  ||  || ||||||||| ||||||||||| ||||||||||| || ||||||||||| || |||||||||||||| ||
-------------------------------------------tccgtattaatttctctgccc-----ttttcatttttgtctttgatttaatcaatgatattttttac---------attctaat--------ctatggtttgattcatttggaactttgaagGCTATTGCTGGAGAGGCTGGAGTACCATTTTTCTATAGAGCAGGTTCTGAATTTGAAGAAAT

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|124825286|gb|EH910152.1|EH910152
EST:     CTGGTACTGGAAAGACATTGCTGGCCAAA                         GCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGTA
genomic: CTGGTACTGGAAAGACATTGCTGGCCAAAgtaagttctc ... aattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTG-A
EST: gi|164091126|gb|ES182709.1|ES182709
EST:     GAATTCTTCTAACCGGGGCACCTGGTACTGGAAAGACATTGCTGGCCAAA                         GCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTA
genomic: GAATTCTTCTAACCGGGGCACCTGGTACTGGAAAGACATTGCTGGCCAAAgtaagttctc ... aattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT
                              agttaac  putative branch site (score: 3)
               attgattttacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctcacatagttgttatattgtcgtctcttgttgaattggttattacttattatgagtgtgtgttttcacagtcatattccacttaataataaattcttattacgctaccaatattctgattgattttacaataagttaacacggtttaaattttgaagGCAATTGCTGGAGAAGCTGGAGTACCCTTCTTCTATAGAGCTGGATCTGAATTTGAAGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA