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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaactcacaatcctagaatattggtttcacatggtgacatttctttgatttatggtcttatgtgaaactttgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA

Basic information

species Arabidopsis thaliana
transcript AT1G61800.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g33954.1 (Oryza sativa), 3'ss of exon 2
---gtaaaactcacaatcctagaatattggtttcacatggtgacatttctttgat-ttatggtcttatgtgaaactt----tgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA
   | || |  ||| | ||  ||| |   |    |  || | | |   ||   |  | |      | |||  | | |    ||  |||  ||   || ||| || |||||||| ||||| |||||  ||||||| ||||||||||| || || || ||||| |||||||| || ||||| |||||||| |||||||||||
aaagaaatatacaccagccacgaaaaagtgcacaatttgttcataaacctgacacatcacatcaatctgttcatcgtgtattgctgaaaattcgatgcagGATTCATGGGGGCGATGATCTCGAACCTGGCATTCGTGTTCCGGAACATATTCTCCAAGAAGGGGATGAAGGGCAAGTCGGTGAGCGGGATGAACTACTA

upper sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G009223_T01 (Zea mays), 3'ss of exon 2
--------gtaaaactcacaatcctagaatattggtttcacatggtgacatttctttgatttatggtcttatgtgaaactttgtggaatt--ttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA
        |||  | ||  ||||| | | | |     ||||   |       | ||      | ||   |   |||| || ||| |   |        | ||| || |||||||||||||| || ||  ||||||| ||  ||||||  ||||| || ||||| |||||||| || ||||| |||||||| |||||||||||
ttgtacttgtagcagtcgaaatcccaaactttgtcagtcactctgaacagcatattcagaagaaggg--tgactgaacctgtgttgttgtaacccaccgcagGATTCATGGGGGCAATGATCTCCAACCTGGCATTCGTCGTCCGGACCATCTTCTCCAAGAAGGGGATGAAGGGCAAGTCCGTGAGCGGGATGAACTACTA

upper sequence: AT1G61800.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0116g00760.t01 (Vitis vinifera), 3'ss of exon 2
---------------------------gtaaaactcacaatcctagaata---ttggtttc-acatggtgacatttctttgatttatggtcttatgtga----aactttgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA
                            | ||| | |   ||  | |||    ||| |||  |  || |||   |  | |   ||||||  || |         | ||||||    | | ||  |||||||||||||||| ||||| || ||| ||||||||||||||||||| || || || |||| ||||||||| |||||||| ||  | ||||||||||||||
gtgagaaggattgattaatattaaagattgaaattgatggtctcaaaattctcttgattttgatgtgatgatcatgatatttcttatgggtttttcaagttctgaatttgtgttgctatgttc-tagGGTTTATGGGGGCTATGATTTCAAATCTGGCATTTGTGTTCCGGAACATATTCTCAAAGAGAGGGATGAAGGGGAAGTCTGTTGGGGGAATGAACTACTA

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|116377047|gb|EG419639.1|EG419639
EST:     CGGAGGCTGCGCTCTCGCGGCCATCACCGAGCTTAACTTCAACATCACTG                         GGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCT
genomic: CGGAGGCTGCGCTCTCGCGGCCATCACCGAGCTTAACTTCAACATCACTGgtaaaactca ... ttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCT
EST: gi|116447970|gb|EG490562.1|EG490562
EST:     CGGAGGCTGCGCTCTCGCGGCCATCACCGAGCTTAACTTCAACATCACTG                         GGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCT
genomic: CGGAGGCTGCGCTCTCGCGGCCATCACCGAGCTTAACTTCAACATCACTGgtaaaactca ... ttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacatttctttgatttatggtcttatgtgaaactttgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA
        ctttgat  putative branch site (score: 5)
                                           ttttttttgt  putative PPT
                                         aattttttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaactcacaatcctagaatattggtttcacatggtgacatttctttgatttatggtcttatgtgaaactttgtggaattttttttgtagGGTTTATGGGGGCAATGATATCGAATTTGGCATTTGTGTTCCGGAATATCTTTTCGAAGAAAGGGATGAAAGGGAAGTCAGTGAGCGGAATGAACTACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA