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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcagaatcttcactcacttaaaaaagtcagattaggacacgtatctacttaaacctgctaactacgtaactaaccctagttaatatcactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG

Basic information

species Arabidopsis thaliana
transcript AT1G11260.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G11260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G06420.1 (Glycine max), 3'ss of exon 2
-aatcagaatcttcactcacttaaaaaagtcagattaggacacgtatctacttaaacctgctaactacgtaactaaccctagttaatat-cactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG
 ||  ||     | ||||| |||    |   |  ||   |||  ||| |    |      ||||  |  | | |   |  | || |  |     ||  |||| |||||||||| ||||| ||||| ||||||||||||||||| |||||||| || |||||||| || ||  | ||||| ||| | || |||||||| ||| 
aaactagttatattactcaattatttcatcaatgttgttacaattatttcacca--ttgactaatgattttagttttctgattttacttatgtgatgaacagTCTGTGCCACTCTACCTATCTGAAATGGCTCCATACAAATATAGAGGAGCATTGAACATTGGCTTTCAATTGTCAATCACAGTTGGTATCCTCGTGGCCA

upper sequence: AT1G11260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G30880.1 (Glycine max), 3'ss of exon 2
aatcag--aatcttcactcacttaaaaaagtcagattaggacacgtatct--acttaaacctgctaactacgtaactaaccctagttaatatcactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG
||  ||  | |  ||| | | ||  | |    |  ||   |||  | | |  ||||  ||     |     ||         |   |  | | |  |   |||| |||||||||| ||||| ||||| ||||||||||||||||| |||||||| || |||||||| || ||| | || || ||  | || ||||| || ||| 
aactagttattagtcaattatttctacat-caatgttgctacatttgttttaactttgactaatcattcttgttttctgattttacttgtgtgatga---acagTCTGTGCCACTCTACCTATCTGAAATGGCTCCATACAAATATAGAGGAGCATTGAACATTGGCTTTCAGTTGTCCATCACTGTTGGTATCCTTGTGGCCA

upper sequence: AT1G11260.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv00s0181g00010.t01 (Vitis vinifera), 3'ss of exon 2
-aatcagaatcttcactcacttaaaaaagtcagattaggacacgtatctacttaaacctgctaactacgtaactaaccctagttaatatcactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG
  ||  |||| || | | | | ||  ||  |   |    |    |    | |      || |    |  ||| ||     | ||  | |   |  |||||| ||||||| || ||||||||||||||||||||||||||||||||||||||  | |||||||| |||||  | || || || || || || || || ||| 
ctatttgaatatt-aattattcaattaatgctattattaatttcttggaattgggtattgtttgaaaattaattatggtaattttgtgtttgttattacagTCTGTGCCGCTCTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCCCTCAACATTGGCTTCCAATTATCCATCACTATTGGTATTCTTGTGGCCA

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|116479254|gb|EG521846.1|EG521846
EST:     TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAG                         GCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCT
genomic: TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAGgtccgtcatt ... ctatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCT
EST: gi|124907351|gb|EH981431.1|EH981431
EST:     TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAG                         GCTGTGCCACTGTACCTCTCTGAGATGGCT
genomic: TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAGgtccgtcatt ... ctatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCT
EST: gi|125288942|gb|EL303027.1|EL303027
EST:     TCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAG                         GCTGTGCCACTGTACCTCTCTGAGATGGACTCCATACAAATACAG
genomic: TCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAGgtccgtcatt ... ctatttacagGCTGTGCCACTGTACCTCTCTGAGATGG-CTCCATACAAATACAG
EST: gi|301502820|gb|HO208360.1|HO208360
EST:     TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAG                         GCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCT
genomic: TCATCGTCGGTCGTATCTTGCTTGGTTTCGGTATCGGTTTCGCTAATCAGgtccgtcatt ... ctatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacttaaacctgctaactacgtaactaaccctagttaatatcactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG
                                    ttaatatcactattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcagaatcttcactcacttaaaaaagtcagattaggacacgtatctacttaaacctgctaactacgtaactaaccctagttaatatcactatttacagGCTGTGCCACTGTACCTCTCTGAGATGGCTCCATACAAATACAGAGGAGCTTTAAACATTGGTTTCCAGCTCTCAATTACAATCGGAATCCTCGTCGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
-atcagaa
- - - - - - cactcac
- - - - - - - - - - taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctaaccc