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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagggtttgatttttacgtcaaatgatgtttttttttttttttttgtagaatagttgctgacattgttccactcttgattttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA

Basic information

species Arabidopsis thaliana
transcript AT1G12000.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 2
gtaagggtttgatttttac--------gtcaaatga-tgtttttttttttttttttgtagaatagttgctgacattgttccactcttgat-tttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA
|||| |  |    || ||         ||  ||| | ||||||  || |   | |||   |    |   ||   |||||  | | |  |  |||| ||| ||  | ||||||||||||||||| | |||  |||| |||||||| || || |||| ||||||||||||||| |||||||| |||||||| |||||  | |   | || ||
gtaaagaataatcttctattgagttgagttgaatcagtgttttgattctgcgtgttgcgtaggtttatgtggttttgttttaatttgaacgtttgattttgg--ttttagATTACCTGCAAGACCTTGCAGAAGGAAGCACATTGTATGGTTTCAGGGGTGGTCCAGCTGGCATCATGAAGTGCAAATACGTTGAACTTACCTCAGACTA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 2
gtaagggtttgatttttacgtcaaatgatgtttttttttttttttttgtagaatagttgctgacattgttccactcttgattttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA
|||| | | |  ||||    ||  ||   |||     |  |||| || |        | ||     | ||    | |   |||| |||||  ||| |||||||||||||||||||| ||   ||| ||||| || ||||| ||||| ||||| || ||||| || ||||| |||||||| |||||  | | | |||||||
gtaacgctctcgttttcgaatccgattcagttaaacgtgcttttcttctt---cttcttcttcttcttttgagatttaactttttttttcttcgtcttagATTACCTGCAAGAGCGCGCACCAGGAAGCACGTTGTACGGTTTCAAAGGTGGACCTGCTGGCATTATGAAGTGCAAATACGTTGAACTCACTTCTGAATA

upper sequence: AT1G12000.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 2
gtaagggtttgatttttacgtcaaatgatgtttttttttttttttttgtagaatagttgctgacatt-gttccactcttgattttgttttcggcgt-gttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA
|| ||| |    |    |  |       |  | |  ||||   | ||||    | | ||  || ||| |||  | |  |||||||   || |  || | |||||||  ||||  | | || |||||| |||||| | || ||||||||||||||||| ||||| |||||||| ||||||||||||||  |  |  |||||| 
gtgaggatcgattcgacatatttggatcttgtgtgattttgactcttgt----ttgatgtggaaattcgttggaataatgatttttcgtttgttgtcggtagATTATTTGCAGAATCATGTGAAAGGAAGCACACTGTATGGGTTCAAGGGTGGTCCCGCTGGGATCATGAAGTGCAAATATGTTGAACTCGACTCTGAATT

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|86069454|gb|DR365211.1|DR365211
EST:     GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTG                         ATTACCTGCAAGAG
genomic: GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAG
EST: gi|124990239|gb|EL062508.1|EL062508
EST:     TCTGGACTGTTTG                         ATTACCTGCAAGAGTCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGT
genomic: TCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAG-CGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGT
EST: gi|124797523|gb|EH887202.1|EH887202
EST:     GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTG                         NTTACCCGCAAGAGCGTGCGAAAGGTAGCAC
genomic: GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCAC
EST: gi|124959147|gb|EL033851.1|EL033851
EST:     TCTGGTAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTG                         ATTACCTGCAAGAGCGTGCGAAAGGTAG
genomic: TCTGG-AGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAG
EST: gi|116438055|gb|EG480647.1|EG480647
EST:     GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTG                         ATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTG
genomic: GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTG
EST: gi|86069448|gb|DR365205.1|DR365205
EST:     GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATATCTGGACTGTTTG                         ATTACCTGCAAGAGCGTGCGAAAGGTAACACATTTTATGGGTTTCA-GGGT
genomic: GTCTGGAGGTCAGGCACCTGGTGGGCACAATGTTATTTCTGGACTGTTTGgtaagggttt ... ggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTT-CAAGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagaatagttgctgacattgttccactcttgattttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA
                                  attttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagggtttgatttttacgtcaaatgatgtttttttttttttttttgtagaatagttgctgacattgttccactcttgattttgttttcggcgtgttagATTACCTGCAAGAGCGTGCGAAAGGTAGCACATTTTACGGGTTCAAGGGTGGTCCAGCTGGTATCATGAAATGCAAATATGTTGAGTTGAATGCTGAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG