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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT

Basic information

species Arabidopsis thaliana
transcript AT1G79000.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 8
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctattt-gtttgatctagtgattctt--tgtta-gaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                                                                | | || | |  |   |||  |  |   | | ||| | ||   || | |||  |   ||||         |||   || | |||              || ||||    |||||    |||||| |||||||||||||||| || ||||||||||||||||| ||||| || ||| | ||||||||||  || ||||  |
----------------------------------------------------------------tgacttctctcctgtaattgagaatagaccactgacttttgccgtcatgaaggaaattattctcatcacttttaaattctatttattccttatttgttagGTTCCTGGAGCCGAAGGTCTTGTGGTTAGAGTTGTTTCATCAGTGGACAAGAAGCTGGAAGTAAAACCACGTTTTTTGGAAATTTTTCAAGAAGATAACT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os06g49130.2 (Oryza sativa), 3'ss of exon 7
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacga--acagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                                                          |||   | |   | || ||   |      |  | || |  || |||  |   | |   | || ||   |  | || |||  || |    ||   || |    || ||||    || ||    |||||| | |||||||||||||| || |||||||| |||||||| ||||| |  ||| |  | ||||| |  ||||| | ||
----------------------------------------------------------agcatatgacactaatattctcaacaaaatattgtattccttattttctt--atctacaaatagatatt--ccttatttactcctaattttcccaccatgttagGTTCCTGGAGCAGATGGACTTGTGGTCAGAGTTGTTTCATCAGTGGACAAGAAACTGGAAGTTAAACCACATTTTTTCAAGATTTTGCAAGAGGACAATT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G139977_T02 (Zea mays), 3'ss of exon 1
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                                                ||     ||   ||  || |||||    |    ||||  |  |    ||||    | |      || |  ||  |   |   | |  || | |||| | ||| ||      ||||||    || ||    |||||  | |||||||||||||| || || ||||||||||| || ||||| || ||| | ||||||||||  || || |  |
-----------------------------------------------gcattatggcgcacttattctttttgccatcaagtttgactcctggtatgatgtccttt------cactccatcaagtttacttctaattatgcttt-atttgtta------gATTCCTGGAGCGGAAGGACTTGTTGTCAGAGTTGTTTCATCAGTGGATAAGAAGCTGGAGGTTAAACCACGTTTTTTAGAAATTTTTCAAGAAGACAACT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G00230.1 (Glycine max), 3'ss of exon 8
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctcttt-atttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                                                  | | |      ||||  || || ||| ||  | |||||    ||||    || | |||    |  |  ||      || | ||  | ||  ||| ||  || |     ||||||||    || ||  | ||||| || |||||||| |||||||||||||| ||| | ||||| ||||| || ||||| || ||||||| ||| || | ||
-------------------------------------------------gcttttaatgtttcttggatattgattattacacttgttg---ctagcatatcctggttttctatggatta------ctaatttcatattcgcttggatgtgttgt---cagATTCCTGGAGCTGAAGCTCTTGTTATAAGAGTTGTGTCATCTGTTGACAAAAAGTTAGAAGTGAAACCGCGGTTTCTGGAGATTTTTCAGGAAGAGAATT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 7
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                                                          |  |||    |  |   ||  | |    ||  | ||   |   | ||    || ||| ||  | |   || |  | || |  |||| || |  |     ||| || |    || ||  | ||||||||||||||||| ||||| |||||||| ||| ||||||| || |  || || |||||||||||||  || || | ||
----------------------------------------------------------aattctactgtcatggattcttgtgaaatttttttacctagaatgtgc--aaatcagaattctaagtgtgccaattttctcccttttacattgttttgccagGTTGCTGGAGCTGAAGCACTTGTGATTAGAGTTGTCTCATCAGTTGACAAAAAGTTGGAAGTGAAGCAGCGGTTCCTTGAAATTTTTCAAGAAGAGAATT

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S404_36V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtaatttaatggtggagtttgtta-acgtttatttctttca---tttattttcacatctgcaagctct--ttatttttatttttctatttg------tttgatctagtgattct--ttgttaga-aacagtatattgaag---ctgactttgttttttctt-tgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT--------
             ||  |  | |    | |  | ||  |    | ||| |||||   ||| |  ||  ||    ||| | |  | |   | |||  |   |  |      |  ||   ||  || ||   |||  || | |  |  |||| |     | ||  |      || | |||    ||      || |  ||| ||| ||| |  | ||| |||||||||| || || || ||||||||||||||||||||||  || ||  | ||||||||||  |  |||  |         
gtacttgcatgtggttttccagttactgtggctattctaaaaatttttgtttcaagttttgtaatcgaattcttaagttttattcaacctcattcatgactaagaaaaaatcagaaaaagcaatgctgcctgtctgacagcgatcgattgtatgctttaacgctaacaagtcatatgatactatgaatgtaggtggccagTGCAGAGGCTTTGGTGGTTAGAGTTGTATCCTCCGTGGACAAGAAGCTGGAAGTCAAACAACGGTTCTTGGAAATTTTTCAAGGAGATTATCCAACTGAG

upper sequence: AT1G79000.2 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S193_70V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttct---atttgtttgatcta-gtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                             ||| ||  ||  | |  |||| |         |    |  || | |   |  |||   |   | ||| ||||| |||      | |||    | | | |   |   ||| || |       |  |  |   |   |   ||  | | |||    ||  |   || || ||| ||| ||| || | ||| | |||||||| || ||||| |||||||||||||||||||| |  || ||| | ||||||||||  || ||    |
gtacttgcacgtgcttttatttagttactgtagtt--attcttggatttgatctttcgagctgtcatgtttcaatcctatgtctttcacgaccttagttttaatttcgacagaattgcaaaagcaatgctgtctcttgctacatctccattgcttgattagtgctgacttgctgtatgatactatgagtttagGTTGCCAGTGCAGAGGCCTTAGTGGTCAGAGTTGTGTCCTCTGTGGACAAGAAGCTGGAAGTCAAGCAACGGTTTTTGGAAATTTTTCAAGAAGAAGACT

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|116465026|gb|EG507618.1|EG507618
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116428303|gb|EG470895.1|EG470895
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116462330|gb|EG504922.1|EG504922
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|124945699|gb|EL021684.1|EL021684
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGT
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGT
EST: gi|116447334|gb|EG489926.1|EG489926
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116414729|gb|EG457321.1|EG457321
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116455249|gb|EG497841.1|EG497841
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116418401|gb|EG460993.1|EG460993
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
EST: gi|116447332|gb|EG489924.1|EG489924
EST:     AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAG                         ATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG
genomic: AGCAGGAAAGAACAGAGAGAGCCAGGGCTCAAGGAAAAAGTTATGATGAGgtaatttaat ... atacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT
                         tttgttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttaatggtggagtttgttaacgtttatttctttcatttattttcacatctgcaagctctttatttttatttttctatttgtttgatctagtgattctttgttagaaacagtatattgaagctgactttgttttttctttgacttgatacgaacagATTCCCACTGCCGAGTCCCTTGTGATTAGAGTTGTTTCATCTGTTGACAAGAAGCTGGAAGTCAAACCTCGATTTCTTGAAATTTTTCGGGAGGATAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT