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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatcccggttcttctttgtttactccagttcatagattgaaaacgctggactttggtgtcatacgtttttgtttattatagatagtaacaatcttttctcattaaattctcaactttcacattcgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTTGAAGTTCTTTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G70730.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 11
gtatgcatcccggttcttctttgtttactccagttcatagattgaaaacgc--tggactttggtgtcatacgtttttgtttattatagatagtaacaatcttttctcattaaattctcaactttcacattcgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTTGAAGTTCTTTGAG
                                    |  ||    |   ||  |  ||||    |||| |   ||||  | |    |  ||  || |    | |   |    ||  | | || |     |   |||||||||||||||| || |||||||| |||||||| || || || || |||  | | ||||||||||||
------------------------------------actgaccatatttgcagtaaacttctaagtcaga-acttttaatgaaaggatgtaa-aataccgctgtgctaccttatgttgatctattga--taaaattgcagGAGCATGCCCACATCAGCTGCCCTTGATGTTGTCGCTAAGAATTTGAATCTCAAGTTCTTTGAG

upper sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 11
gtatgcatcccggttcttctttgtttactccagttcatagattgaaaacgctggactttggtgtcatacgtttttgtttattatagatagtaacaatcttttctcattaaattctcaactttcacattcgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTTGAAGTTCTTTGAG
                    ||| |  | ||   |  ||   || |       ||| || |    || | |||    ||  | ||   | | | |  ||  |  |   ||         | | |  ||   | |||||||||||||| || |||||||| |||||||| |||||||| || |||  | | ||||||||||||
--------------------ttgat--cccccacttgta---tgcagctatctgaccttag----atgcatttaaaatttctctatgcactgataggctacttacgacaa---------tctaatgttgtaaatgcagGAGCATGCCAACATCAGCTGCCCTTGATGTTGTTGCAAAGAATTTGAATCTCAAGTTCTTTGAG
















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|125252157|gb|EL266242.1|EL266242
EST:     CTGTTGGGGCCATACCATACTTCAGCTCTGGTTTAAAAGGTGTTGCTAG                         GAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTT
genomic: CTGTTGGGGCCATACCATACTTCAGCTCTGGTTTAAAAGGTGTTGCTAGgtatgcatcc ... cgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTT
EST: gi|116415445|gb|EG458037.1|EG458037
EST:     GCTGTTGGGGCCATACCATACTTCAGCTCTGGTTTAAAAGGTGTTGCTAG                         GAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTT
genomic: GCTGTTGGGGCCATACCATACTTCAGCTCTGGTTTAAAAGGTGTTGCTAGgtatgcatcc ... cgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagatagtaacaatcttttctcattaaattctcaactttcacattcgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTTGAAGTTCTTTGAG
    tagtaac  putative branch site (score: 1)
               ttttctcattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatcccggttcttctttgtttactccagttcatagattgaaaacgctggactttggtgtcatacgtttttgtttattatagatagtaacaatcttttctcattaaattctcaactttcacattcgtattgcagGAGCATGCCGACCTCAGCTGCACTTGATGTCGTTGCAAAAAACTTGGGTTTGAAGTTCTTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG