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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttaaccagctcaattactcctctcttaaacaaattgtagttaaaaaagagagtctaagttcaggtttgggtttgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA

Basic information

species Arabidopsis thaliana
transcript AT2G42600.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os08g27840.1 (Oryza sativa), 3'ss of exon 8
----------------------------------gtaagttcttaaccagctcaattactcctctc--ttaaacaaattgtagttaaaaaagagagtcta------agttcaggtttgggtttgtatta---tagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
| || | | | | || ||| | || |||||| | | || | | | | | | || || ||| || | |||||||||||||| | ||||||||||||||||| ||||||||| | ||||| || | || || || || || |||||||| || ||||| ||||| ||||
gtgagtgttttgtttcttcataatcatcagacttggaacatttcatataatgcatttaaggcacttagctaaacattgttcatttcaggcaaaacctttgtaaattaattttctttacatttttcatgaaatcagGCAACACCAGAGATGGAGTATGGAAGGATGAATATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGTGGTGGCATCGAGTCACTCCGTGCCATCCCATGGA

upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os09g14670.1 (Oryza sativa), 3'ss of exon 8
---gtaagttcttaaccagctcaat--tactcctctcttaaacaaattgtagttaaaaaagagagtctaagttcaggtttgggtt-----tgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
| | | | ||| || || || | | | |||| | ||| | | || || || |||| ||| || | |||||||||| ||| ||||||||||||||||||||||||||| | ||||| || | || || || ||||| || || || || ||||| ||||| ||||
atggaacagtgtaaactagactaaagataaccttggagccattgaattagacttattagactttttcaaaattataatttgtgttgtttgtggttggcagGCAACACCTGAGACAGAGTATGGAAGGATGAACATAGGAAGCAGGCCATCCAAGAGGAAGCCGAGTGGAGGCATTGAATCACTCCGTGCGATCCCATGGA

upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 8
-gtaagttcttaaccagctcaattactcctctcttaaacaaattgtagttaaaaaa----gagagtctaagttcag-gtttgggtttgtatt----atagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
|| || || | | | |||| | || | | ||| | | |||| | || | || | |||| | ||||||| |||||| | |||||||| ||||||||||| |||||| | ||||| ||| | || || || | || |||||||||||||| |||||||| ||||
tactcctttgtagtaccctgtaaaattttcatcttgttttggtagtgggtcaaattttctgcgtaactaatcctggcattcgtgtctttatttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA

upper sequence: AT2G42600.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G473001_T01 (Zea mays), 3'ss of exon 8
-gtaa--gttcttaaccagctcaattac--tcctctcttaaaca----aattgtagttaaaaaagagagtctaagttcaggtttgggtttgtatt-atagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
| || | || | ||| || || | | || || || | ||| | | || | || | | | |||||| || | ||||||| || || |||||||| |||||||||||||||||| | ||||| || | || || |||||||| ||||| || || || |||||||| ||||
agaaactatcttttgcaagcctaagtaaaatggttactgaagcattcgatttgacccctacatttagcgagtatttactttgtgatgtttgtgttgacagGCAACCCCTGAAACAGAGTATGGTAGGATGAACATAGGAAGCAGGCCATCCAAGAGAAAGCCGAGCGGAGGTATCGACTCACTCCGAGCAATCCCATGGA

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|86065050|gb|DR360807.1|DR360807
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCGAGTTATGGAAGGATGAACATAGGAAGCCGACCATC
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCGAGT-ATGGAAGGATGAACATAGGAAGCCGACCATC
EST: gi|124749862|gb|EH839992.1|EH839992
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
EST: gi|164205988|gb|EL975482.1|EL975482
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCG
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCG
EST: gi|86065049|gb|DR360806.1|DR360806
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
EST: gi|86068615|gb|DR364372.1|DR364372
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCA
EST: gi|124816329|gb|EH901195.1|EH901195
EST:     ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTG                         GCAACACCAGAGCTCGAGTATGGAA
genomic: ACCGTTCTGTTGTCTTCAAGGAGCCCCGTTTTGTTGAGTACTTCCGTCTGgtaagttctt ... tgtattatagGCAACACCAGAGCTCGAGTATGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaaattgtagttaaaaaagagagtctaagttcaggtttgggtttgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA
     attgtagttaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttaaccagctcaattactcctctcttaaacaaattgtagttaaaaaagagagtctaagttcaggtttgggtttgtattatagGCAACACCAGAGCTCGAGTATGGAAGGATGAACATAGGAAGCCGACCATCAAAACGTAAACCAAGCGGAGGAATCGAGTCGCTGCGTGCAATCCCGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA