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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttcaatatgccaattttggaatcgtactagctattactgtatttctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA

Basic information

species Arabidopsis thaliana
transcript AT4G16155.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 1
cttcaatatgccaattttggaatcgtactagctattactgtatttctt-tacggtattcatgatctcatcgagtgattgttgttttgat-aacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
    || ||  ||   ||  ||  ||| || |   | |  |||| ||  | |  || |  ||     ||    | | ||||   | |   ||  ||||  ||||  | |||||||| || ||||| ||||||||||| || || ||||| || |||||||| ||||| || || ||||| || |||||||| || ||| | |
--ataagattgcagagttataaatgtaataacctgttcgttattactagtccactactgctgtctcaatgtgttaagtgttaactggcccaaatttgtgcagGGTTTGAAAACTGCAATTATTGAGGGAGATGTTGTAGGTGGGACTTGTGTAAACAGAGGTTGTGTCCCATCAAAAGCACTTCTTGCTGTCAGCGGTCGCA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G145595_T02 (Zea mays), 3'ss of exon 1
cttcaatatgccaattttggaatcgta-cta-gctattactgtatttctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
      | |    |   ||||    || ||| |||   |     |    | ||    |  || |  |  |  | ||||| |||     ||  | |  | |||||  | |||||||| || ||||| ||||| || || || || ||||| || |||||||||||||| || || || ||||| |||||||| ||||||||||
-ccatgtgttttgaacatggacctttatctatgctgccagcaattgaactcacatattcaataagtttttttaatgatttttgaaaaaatgtc-tcatgtagGGTTTGAAAACTGCCATAATTGAGGGAGACGTCGTGGGTGGAACTTGTGTCAACAGAGGCTGTGTTCCGTCAAAGGCTCTCCTTGCTGTAAGTGGTAGGA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 1
----cttcaat-atgccaattttggaatcgtactagcta-ttactgtatttctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
        ||| |||||||   |  || | ||| |   | || ||     | |  || |  |  ||  |    | |  | | |  || | | ||    ||||  ||||  | ||||| || || ||||| ||||||||||| || || ||||| || |||||||||||||| || || ||||| || |||||||| || ||| | |
caaagaagaatgatgccaaacatt-aaccataccaataaatttctaagagtttgcactgcttctatattgatcttgtttcact-ctgctctaat----ttgttcagGGCTTAAAAACAGCAATAATTGAGGGAGATGTTGTGGGTGGGACTTGTGTAAACAGAGGCTGTGTCCCATCGAAAGCGCTTCTTGCTGTCAGCGGTCGAA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 1
cttcaatatgccaattttggaatcgtactagctattactgtatttctttacggtattcatgatctcatcgagtgattgttgtt-ttgataacgttgt-atagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
  | |||     || ||   | ||||    |||     ||   |    || | |    || |  |  | | | ||| | | || || |   | |  |   ||||  | ||||| || ||  | ||||||||||| || ||||| || || || |||||||||||||| ||||||||||||||  | || || |||||| | |
-atgaat-caagaaattgatagtcgttgatgctgactgtgggataaagtaagttgagtatcacatttttgtgagataggttttattaacggcatgattgcagGGTTTGAAAACAGCCATTGTGGAAGGAGATGTGGTGGGAGGGACATGTGTGAACAGAGGCTGTGTTCCTTCCAAAGCTCTTTTAGCCGTGAGTGGTCGTA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 1
cttcaatatgccaattttggaatcgtactagctattactgtatttctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgta----tagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
  |  ||| |||  |  || |     | |    | | | | ||    | | | |    || |  |  | | | ||  |  |||||  ||||| | |      ||||  | ||||| |||||  | ||||||||||| || ||||| || || || ||| |||||||||| ||||||||||||||  | || || |||||| | |
aattgata-gccgttaatgaatattgaatgctgactgcgggatagagtaa-gttgagtatcacatttttgtgaga--gaagttttattaacggtatgattgcagGGTTTGAAAACAGCTATTGTGGAAGGAGATGTGGTGGGAGGGACATGTGTGAACCGAGGCTGTGTTCCTTCCAAAGCTCTTTTGGCCGTGAGTGGTCGTA

upper sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 1
--------------------------------cttcaatatgccaattttggaatcgtactagctattactgtatttctttacggtattcatgatctcatcgagtgattgt-tgttttgataacgttg----tatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
                                  | | || | |   ||  |   ||| ||     |   |     ||     ||  ||     | || | |  |   ||  ||  ||| |  | |||       ||||  | || || || ||||| || || || |||||||| |||||||| || ||| |||| ||||||||||| ||||||||  | ||||| |||||  | |
gtaggacggctggatccatattttgctccgtttgtgagtacgtcgtgttgagcgacgtcct--tcgtggtttctgctcaaccgggcgttggatgtatcgtgggtttgatgcgtggattggtggcattggcaacgcagGGGTTGAAGACGGCGATCATCGAGGGGGACGTTGTTGGCGGTACTTGTGTCAACCGAGGGTGTGTGCCTTCGAAAGCTCTCTTGGCTGTGAGTGGGCGTA

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|125020361|gb|EL092630.1|EL092630
EST:     TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAG                         GGACTCAAAACTGACTATCATTGAAGGAGATGTTGTTGGA
genomic: TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAGgtcctctttc ... cgttgtatagGGACTCAAAACTG-CTATCATTGAAGGAGATGTTGTTGGA
EST: gi|86060709|gb|DR356466.1|DR356466
EST:     TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAG                         GGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTT
genomic: TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAGgtcctctttc ... cgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTT
EST: gi|124997507|gb|EL069776.1|EL069776
EST:     TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAG                         GGACTCAAAACTGCTATCATTGAAGGAG
genomic: TCGGAGCTGGAGTTGGTGGCCATGGAGCTGCATTGCACGCCGTCGAGAAGgtcctctttc ... cgttgtatagGGACTCAAAACTGCTATCATTGAAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA
                                       tgataac  putative branch site (score: 2)
                                    ttttgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttcaatatgccaattttggaatcgtactagctattactgtatttctttacggtattcatgatctcatcgagtgattgttgttttgataacgttgtatagGGACTCAAAACTGCTATCATTGAAGGAGATGTTGTTGGAGGTACTTGCGTTAACAGAGGCTGTGTGCCTTCCAAAGCTCTACTTGCTGTTAGTGGTAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - -attttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg