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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA

Basic information

species Arabidopsis thaliana
transcript AT1G01050.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g59040.3 (Oryza sativa), 3'ss of exon 6
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactc-caatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
||| |   |  |||       |   |  |    |         |       |  | || ||| | |  ||||      | || ||||  | || ||| |||||       || ||   ||||||| || ||||||||||| || ||||| |||| |||||||||||||||    || |||| ||||||||  || ||  |||||||||| |||   || |
gtatattttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgtttt-----ttttttactgacgatattggatttt-------gtgatc--agGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g59040.2 (Oryza sativa), 3'ss of exon 5
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtact-ccaatcttgtatttttggcgctgtaattt-----tagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                               ||||| | ||| |  |  |    ||       |  | | || | |  | ||||  |     | || || |   |    || | |||      ||||||| || ||||||||||| || ||||| |||| |||||||||||||||    || |||| ||||||||  || ||  |||||||||| |||   || |
-------------------------tttctactgttctgtttgtagcaaagggaaaaagacctgcacgggttcactctttttgttttgttttttttttactgacgatattggattttgtgatcagGGTGAGAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCATTACAATGACATCAGTGAGCTGTCTCCTCACCGCCTCCAAGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G061928_T04 (Zea mays), 3'ss of exon 6
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                     |           |    | |||    |      ||     |   || | ||  |   | ||  |  | |    | | | || |||| |||      |||||||||| ||||||||||| || ||||| |||| ||||||||||||||||   |||||||  |||||||  || ||  ||||||| || ||    || |
--------------------gtatttcacgctagacactatttgaggtagagggaaaagaatgactctgctttgactctgtttcaaactatggctatctgttgggcgttgt-----cagGGTGAAAAGGATGACAAGATAATAGCAGTCTGTGCTGATGATCCTGAATATCGTCACTACAACGACATCAGTGAGCTGTCTCCTCATCGCCTGCAAGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 6
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
              |  |  |||  |   |||| ||| |  |            |||     || || | ||  |    |||||  || || |||| |||| ||  |  |   | | |||||||||| ||||||||||| || ||||| |||| |||||||||||||||    |||||||  |||||||  || ||  |||||||||| ||    || |
-------------gtatttcatgttacagctctatttgtggta------gagggaatagaagagctctgcttcga----cttgt-ttctaaccttggatttctgttgg-gcgttgtcagGGTGAAAAGGATGACAAGATAATAGCAGTATGTGCTGATGATCCTGAATACCGTCACTACAACGACATCAGCGAGCTGTCTCCTCACCGCCTGCAAGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 6
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                          | | ||| ||   | |||  || |    ||   |  |  |  |||  ||   | |       ||||       || |     ||| |    |||| || || ||||| || || |||||||| |||| ||||||||| |||||||||||||| |||||| ||||||||||||| ||||| || |||   || |
------------------------gtatattctcttggctctttagctgataaaaaaattgaaattttgttccaaccatttaaa----caataacaagcttgtccaattgtgacac-agGGGGAGAAGGATGATAAAATTATTGCAGTATGTGCTGATGATCCAGAATATAAGCACTATACTGACTTCAAAGAACTTCCACCTCATCGCCTCATGGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 5
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
           |||  || |||  |       || ||| ||   |  | |  | || | |||     |    ||||     | || |    | ||| |  |||||| |   |     |||| || |||||||| || |||||||||||||||| |||||| || |||||||||||||  ||||||   | ||||||| | ||||| ||  |||| || |
---------gtactgaattaattta------ttgctttcttagccaatgaaaccaaccatttccacaataacaaatacaaatataatgtggtattg-acatttggctcaaca----cagGGAGAGAAAGATGATAAAATCATTGCAGTGTGTGCTGATGACCCAGAATATAAGCACTTTACTGACTATAGAGAACTTGCACCTCATCGCATCTCCGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA03G42280.1 (Glycine max), 3'ss of exon 6
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                   | ||||   | |  | ||| ||  ||  | |  | || |  | |   |    | ||         |    ||| | |||||            | |  |||| || |||||||| || |||||||||||||||| |||||| || |||||||| ||||  || |||   | ||||||| | ||||| ||  ||||||| |
-----------------gtattgaattcatt--gatttcttagtcaataaaaccaaccaatcattcccacattaacaaata---aaattaatgtggtattgacatttgaaataatacagGGAGAGAAAGATGATAAAATCATTGCAGTGTGTGCTGATGACCCAGAATATAAACACTTTACAGACTATAGAGAACTTGCACCTCATCGCATCTCTGAGA

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA18G18510.1 (Glycine max), 3'ss of exon 5
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
           |||  || |||  |       || ||| ||   |  | |  | || | |||     |    ||||     | || |    | ||| |  |||||| |   |     |||| || |||||||| || |||||||||||||||| |||||| |  |||||||||||||  ||  ||   |||||||||                      
---------gtactgaattaattta------ttgctttcttagccaataaaaccaaccatttccacaataacaaatacaaatataatgtggtattg-acatttggctcaaca----cagGGAGAGAAAGATGATAAAATCATTGCAGTGTGTGCTGATGACCTAGAATATAAGCACTTTACCAACTATAAAGAACTT----------------------

upper sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                           ||     ||| | |         |    | || |||| ||     |    ||   |   |   |  ||   || ||    |    ||   |||| || || || || ||||||||||| || || | ||| ||||| ||||||   |||||||||||||||||||| ||||| |||||  | ||  |||| |
-------------------------gtgatgtcatttctctcaagcaaatcatgcaaccattagttcttcacagtgagttgaggcatatgaaattcagttctttattc----ataccagGGAGAGAATGACGATAAGATCATTGCTGTATGCGCTGACGATCCAGAATATCGACACTACACTGACATCAAAGAGCTTCCACCTCATAGACTAGCTGAGA

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|152033655|gb|BP561551.2|BP561551
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|125180360|gb|EL197398.1|EL197398
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGA
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGA
EST: gi|86084748|gb|DR380507.1|DR380507
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|164210201|gb|ES179229.1|ES179229
EST:     GCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGAGTCATTGCAGTGTGTGTTGATGATCCT
genomic: GCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGA-TCATTGCAGTGTGTGTTGATGATCCT
EST: gi|164038778|gb|ES113165.1|ES113165
EST:     GCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGT
genomic: GCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGT
EST: gi|125040845|gb|EL113114.1|EL113114
EST:     TAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: TAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|47828474|gb|CK118158.1|CK118158
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|124961084|gb|EL035678.1|EL035678
EST:     AATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: AATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|86078040|gb|DR373797.1|DR373797
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|125112057|gb|EL163299.1|EL163299
EST:     ATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
genomic: ATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATAT
EST: gi|164217779|gb|ES089629.1|ES089629
EST:     CGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCC
genomic: CGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCC
EST: gi|125166735|gb|EL192394.1|EL192394
EST:     GTTGTTTTCTGCGTGTCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTG
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTG
EST: gi|124986488|gb|EL059006.1|EL059006
EST:     GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAG                         GGTGAAAAAAGATGACAAGATCATTGCAGTGTGTGTTG
genomic: GTTGTTTTCTGCGTGCCAGAGCCATTGGATTAATGCCTATGATTGACCAGgtaaaaccta ... gtaattttagGGTGAAAAA-GATGACAAGATCATTGCAGTGTGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA
                         aatcttgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaacctaaacttgatcaatgaaaagactctgttttttttttctcttactctaatcctttaggtcagtttaaatggtcttgtactccaatcttgtatttttggcgctgtaattttagGGTGAAAAAGATGACAAGATCATTGCAGTGTGTGTTGATGATCCTGAATATAAGCACTACACTGACATCAAAGAACTTCCTCCTCACCGTCTCTCTGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC