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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT

Basic information

species Arabidopsis thaliana
transcript AT4G38920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: AC216067.3_FGT002 (Zea mays), 3'ss of exon 1
aattatgctttttcttcatatcgaag---gcatgttgattacttgtgtaaacca--tagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
 ||| || |         | | | |      |  | ||   | | |      ||   ||  || |  ||||     |   |||   | |   || |   |   ||| ||||| || ||||||||||| || ||||| || || || ||||| || |||||||||||| |||||||| | || |||||||| || || || || ||
gatt-tggtccgatcgggtgtgggatttcagaaatcgacagccttttcccgtcagacaggcaggtcctgact----acgctgttcttttgcttgatccgatgcagGCATGGGCGCAGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G177005_T01 (Zea mays), 3'ss of exon 1
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
   |  | |      |||    |  ||  |   ||   |    |         ||  |   ||  |     ||  |||   | |   || |       ||| ||||| || ||||||||||| || ||||| || || || ||||| || |||||||||||| |||||||| | || |||||||| || || || || ||
tggtccgatcgggtgtcagtctgtcggattccagaaagcggtgggctttttcggtcgggcagttgctgactaggctgttattttgcttgatccggcgcagGCATGGGCGCCGCGTACGGGACCGCGAAGAGCGGCGTCGGCGTGGCGTCGATGGGTGTGATGCGGCCGGAGCTCGTCATGAAGTCCATCGTGCCCGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S2_120V6.1 (Physcomitrella patens), 3'ss of exon 1
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaaca-agGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
       || | ||    |   ||| |   |  |||     ||| |     | ||    ||||||            || |      |||| ||  |  ||| ||||| ||||| || || || || || ||||| || |||||||||||||||||||| ||| | || ||| | ||||||||||| || |||||||| ||
gccaccactgtgtcactgttgggaaagtgagacgatgtgcagtgaatcattttgtacagttgtgaaaccgcgttccttg-actacgatgttgttggcgcagGCATGGGCGCTGCCTATGGAACGGCCAAAAGTGGAGTTGGAGTGGCATCTATGGGTGTCATGCGACCTGAGCTAGTGATGAAGTCCATCGTCCCAGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S45_100V6.1 (Physcomitrella patens), 3'ss of exon 1
aattatgctttttcttcatatcgaaggcatgt-tgattacttgtgtaaaccatagttagattgt--gaccttaaagagtgtgtatctttgtg-----ttattaaca-agGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
               | |  | || ||| | | |  ||  ||      ||  |  | || |||   |  ||| |    | |||      | |     || | | |  ||| ||||| ||||| || || ||||| |||||||| |||||||||||||| |||||||||||| |||| ||| ||||||||||||| || || ||||| ||
---------aagcagtgacgttgagggcctatcttgttgttttgaaggactttgatcagcttgctcgctctttaccgatatgttaacccgaggaggtttttgagcgcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCAGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S1_66V6.1 (Physcomitrella patens), 3'ss of exon 1
-aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagtt----agattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
  |   | |    | ||||    | ||   | |   || ||| | |  | | |  ||    |  |  ||  ||   | |  | |  |  ||| ||| | |   ||| ||||| ||||| || || ||||| |||||||| |||||||||||||| |||||||||||| |||| |||||||||||||| ||||| || ||||| ||
gtagcgtacaagattttcaccgtgcag---tttaattttcttatttggagcgtgattttgaacttcctggactctgacaaagcg-gtggttg-gttttgattcagGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCAGAGTTGGTGATGAAATCTATCGTGCCAGTAGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S45_97V6.1 (Physcomitrella patens), 3'ss of exon 1
-----aattatgctt--tttcttcatatcgaaggcat-gttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
     |   ||| |      |    | ||||  || |  |  |  |  ||        ||   |||||  |||  | |||  |||    | |||| |         ||| ||||| ||||| || || ||||| |||||||| |||||||||||||| |||||||||||| |||| ||| ||||||||||||| || || ||||| ||
ataacagcgatgttgggcaccccactttcgagtgcctcatctaggatatggcctcgaaattcctagat-atgaa-taaaatggtgaaggtttttgcgcgc------agGCATGGGCGCTGCATATGGAACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTACCAGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S200_79V6.1 (Physcomitrella patens), 3'ss of exon 1
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatc------tttgtgttatta-acaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
       |   |      | | |    | |     | | ||   | | | |  ||  || |  ||   |   |    || |        |   |||||||     ||| ||||| ||||| || |||||||| |||||||| |||||||||||||| |||||||||||| |||| ||| ||||||||||||| || || || || ||
-------cccgtgaacggtgttgggcacttaagcttcaatttcctcagctagggtgcgacttcgaaactcctggacatgaactaaatgttgaatgttattgcgtcagGCATGGGCGCTGCTTATGGGACAGCCAAGAGTGGAGTGGGAGTGGCATCCATGGGTGTGATGCGGCCCGAGCTGGTGATGAAGTCGATCGTGCCTGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ14420 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------aattatgctttttcttcatatcgaagg------catg---ttgattacttgtgtaa-------accatagtt---agattgtgaccttaaagagtgt-gtatctttgtgttattaaca----agGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
                                                               |  ||    |    ||  |  ||       ||||   | |  | | || |  |        ||| | |    |||||  || |  |||        | |  || ||  |||  |     ||| ||||||||||| || || || |||||||||||||| ||||||||||| ||||| |||||| |||||||| | |||||||| || || || ||||| ||
gtaagttcttgcctctcaccgccatggctggactggatctagggttgtggtgcgtgtctcggctgcgcggcattgcaatgcctgagcttgggccatggattcgccttcctgcgcgatttccttgccacaatcccgagatttcgatcccaaaattccccattttcttatggaattttctttgcagGCATGGGAGCTGCCTATGGAACCGCAAAGAGTGGTGTTGGAGTGGCATCCATGGGCGTGATGCGGCCGGAGCTCGTGATGAAATCGATCGTGCCAGTGGT

upper sequence: AT4G38920.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ26016 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------------------------aattatgctttttcttcatatcgaagg------catg---ttgattacttgtgtaa-------accatagtt---agattgtgaccttaaagagtgt-gtatctttgtgttattaaca----agGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
                                                               |  ||    |    ||  |  ||       ||||   | |  | | || |  |        ||| | |    | |||  || |  |||        | |  |  ||  |||  |     ||| ||||||||||| || || || |||||||||||||| |||||||| || ||||| |||||| |||||||| | |||||||| || || || ||||| ||
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|116466768|gb|EG509360.1|EG509360
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|86025395|gb|DR321148.1|DR321148
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|86025413|gb|DR321166.1|DR321166
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|86025412|gb|DR321165.1|DR321165
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|86025402|gb|DR321155.1|DR321155
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|164189874|gb|ES137009.1|ES137009
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGC
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGC
EST: gi|86025396|gb|DR321149.1|DR321149
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|124748283|gb|EH838413.1|EH838413
EST:     TTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAAGAGTGGTGTGGGAGTGGCATCT
genomic: TTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAA-GAGTGGTGTGGGAGTGGCATCT
EST: gi|164164162|gb|ES027747.1|ES027747
EST:     CGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|301501561|gb|HO207101.1|HO207101
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|124729683|gb|EH821085.1|EH821085
EST:     GCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
genomic: GCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTA
EST: gi|125285960|gb|EL300045.1|EL300045
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAG
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAG
EST: gi|125156767|gb|EL186211.1|EL186211
EST:     CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCAT                         GTATGGGAGCTGCGTACGGGACAGCAAAGAGTG
genomic: CGCTCCTTTCTTCGGCTTCCTTGGCGCTGCCGCTGCGCTCGTCTTCTCATgtatatccat ... tattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT
                                            ttattaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattatgctttttcttcatatcgaaggcatgttgattacttgtgtaaaccatagttagattgtgaccttaaagagtgtgtatctttgtgttattaacaagGTATGGGAGCTGCGTACGGGACAGCAAAGAGTGGTGTGGGAGTGGCATCTATGGGTGTGATGAGGCCGGAGTTGGTGATGAAGTCTATTGTCCCAGTTGT

- - - - - - - - - - - - - - - - - - - - - - - aaccata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttaaa