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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT

Basic information

species Arabidopsis thaliana
transcript AT2G16510.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 1
-attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
 |  ||||   ||        |||| | | ||  | |    ||||      |   | | ||       | |||  |    |     || |||||     ||| ||||| ||||| ||||||||||| |||||||| || || ||||| || ||||| |||||| | || ||| |||| |||||||| || || || |||||
aagcagtgacgttgagggcctatcttgttgttttgaaggactttgatcagcttgctcgctctttaccgatatgttaacccgagga-ggtttttgagcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCAGTGGT

upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 1
attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgatt--gggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
  ||| || |     |   |   || | ||||  | |    ||  ||  ||||||  |        | |   ||| |    | |  | | ||||| ||  ||| ||||| ||||| ||||||||||| |||||||| || || ||||| || ||||| |||||| | || |||||||| ||||| ||||| || || || ||
-gtagcgtacaagattttcaccgtgcagtttaattttcttatttggagcgtgattttgaacttcctggactctgacaaagcggtggttggttttgattc-agGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCAGAGTTGGTGATGAAATCTATCGTGCCAGTAGT

upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 1
--attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaa-atgag-atgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
  |  || | | || |    | | |    |||   ||      |   |  | ||     |     | || | ||||  |   || |   || |||||     ||| ||||| ||||| ||||||||||| |||||||| || || ||||| || ||||| |||||| | || ||| |||| |||||||| || || || |||||
ataacagcgatgttgg----gcaccccactttcgagtgcctcatctaggatatggcctcgaaattcctagatatgaataaaatggtgaaggtttttgcgcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTACCAGTGGT

upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
---attagtgttcttag--atcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
    | |  | | || |  |    |   |  ||||       |    || || |  ||       || | | || | | ||||||  | ||  || | |  | ||| ||||| ||||||||||| ||||| |||||||| || || ||||| || ||||| |||||| | || ||| |||| |||||||| || || ||||||||
cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaa-atgttg--aatg--ttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------------------------------------------------attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattggg-----tcgggcgtaaaatgag--atgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
                                                                             ||   ||  ||| |  ||     | |  ||   |      ||  |       ||   |     |||  |  |||||     || || |||  | |||||  ||  ||| ||||||||||| |||||||| ||||||||||||||||| ||||| || ||||| |||||| | || ||| | || ||||| || || || || |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: AT2G16510.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
-----------------------------------------------------------------------------attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattggg-----tcgggcgtaaaatgag--atgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
                                                                             ||   ||  ||| |  ||     | |  ||   |      ||  |       ||   |     |||  |  |||||     || || | |  | |||||  ||  ||| ||||||||||| |||||||| ||||||||||||||||| ||||| || ||||| |||||| | || ||| | || ||||| || || || || |||||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgatatttcgatcccaaaattccccattttctcatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCGTCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

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|86019203|gb|DR314949.1|DR314949
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019200|gb|DR314946.1|DR314946
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019201|gb|DR314947.1|DR314947
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|124893187|gb|EH972089.1|EH972089
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTT
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTT
EST: gi|86019207|gb|DR314953.1|DR314953
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019212|gb|DR314958.1|DR314958
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019208|gb|DR314954.1|DR314954
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019202|gb|DR314948.1|DR314948
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019211|gb|DR314957.1|DR314957
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019210|gb|DR314956.1|DR314956
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019206|gb|DR314952.1|DR314952
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCG-CGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019205|gb|DR314951.1|DR314951
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|86019204|gb|DR314950.1|DR314950
EST:     TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: TGCTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
EST: gi|125030226|gb|EL102495.1|EL102495
EST:     CTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCT                         GTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA
genomic: CTCCGTTCTTCGGCTTCCTTGGCGCCGCCGCCGCTCTCGTCTTCTCCTgtacgccatt ... ttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT
                    taaaatga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attagtgttcttagatcagaatctggattttaggtattgatttgtgattgtgattgggtcgggcgtaaaatgagatgttgttactggattttggttttagGTATGGGAGCTGCTTATGGAACAGCAAAGAGTGGTGTTGGTGTGGCTTCAATGGGAGTGATGAGACCTGAGTTGGTTATGAAGTCTATTGTCCCTGTGGT

- - - - - - - atcagaa
- - - - - - - - - - - - - - - - - - - gatttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatga