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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagtcttttttgttatctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG

Basic information

species Arabidopsis thaliana
transcript AT3G51870.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 3'ss of exon 4
ttagtcttttttgttatctgtattgaaactgacagcat-tcatc-gttaaggaagatttctgtatt---gaaaatgtgactgatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
                   ||  | |  |  ||    | ||||| || ||  |    || || |||   |  | |   | |      |   |  |||| |||||||| || |||    | || || |   ||||  | ||  | || |||||||| |||||||||||||| ||||||||||||||  | 
-------------------gtgataacgccaactctttatcatcagtcaattacctattttggattcctgtcatttcaatttccatgtacctgctttgcattcagAAATTTTTCCGGAGAAAGGACGGAGAGCTTACTGTGTTTGGGAGACTTGCTGCTGGTGCTTGTGCGGGCATGACATCTACACTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G178460_T01 (Zea mays), 3'ss of exon 4
-----------------ttagtcttttttgtta-tctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaat--gtgact---gatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
                 |||  |||  |  | | | | | || | | |    |   |  |   |     |  | ||| | |   || |  || | |    ||| | ||   ||||  ||||||||  | |||    | || ||||   |||| || ||| | || |||||||| ||||||||||| || ||||||||||||||  | 
gtcatagttactcacggttacacttagtcatcaatttatttttacattctttgtgatagtgagttcttcatttctctctctcataagtcagtaagtcacaatgttactgcttttta-attcagAAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G08120.1 (Glycine max), 3'ss of exon 4
ttagtcttttttgttatctgtattgaaactgacagcattcat--cgttaaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
            |||| ||||  | ||  |     |||  ||  | ||     |   ||   | || |  |  | | | || ||| |  ||||       ||||  | ||||| || || |||| | ||||||| ||  | |||||||||||||| ||||||| ||||||||||||||| ||||| 
------------gttagctgt--taaactttctttcatgaatttcttttccccaatattgcatgttcatgac-taagttatacttttggattta-----tagAAAATATTCAAGGGAAAGGATGGTGAGCTCTCTGTTCTGGGAAGACTTGCAGCAGGTGCTTTTGCTGGCATGACATCAACTTTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G42950.1 (Glycine max), 3'ss of exon 5
ttagtcttttttgttatctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattc--agAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
            |||| |   | | | | |  ||| | |  |  |     |   |  ||||          || ||||    ||||  ||||| ||||  ||||  | ||||  ||  |  |||    ||| || ||    |||||||||||||| ||||||| |||||| |||||||| ||||| 
------------gttaccccaaattatagtatcagaagttctaatggcaaatattacctgttc-------atgtctga-atatctac-ttttggattcacagAAAATATTCAGGGGAGAGAATGGCAGGCTATCTGTTGCGGGAAGACTTGCAGCAGGTGCTTTTGCTGGAATGACATCCACTTTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G18140.1 (Glycine max), 3'ss of exon 4
ttagtcttttttgtta-tctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattca--gAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
            ||||  |  || | |   |  ||| | |  |  |  || ||   ||   | || |     || ||||    ||||  ||||| | |||  |||  | ||||| ||  |  |||   ||||||| ||    |||||||||||||| ||||||| |||||| |||||||| ||||| 
------------gttaacccctaattattgtatcagaagttctaat--agcaaatattacctgttca-----tgtctga-atatctactttttgaactcacagAAAATATTCAAGGGAGAGAATGGCGAGCTCTCTGTTGCAGGAAGACTTGCAGCAGGTGCTTTTGCTGGAATGACATCCACTTTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g02230.t01 (Vitis vinifera), 3'ss of exon 4
------ttagtcttttttgttatctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatg-tgactgatgcttctatattttgtattc-agAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
       | |     | | | | |   ||| |   ||     ||  || | |    | ||||  ||| |   | ||  ||| |  |  || || |  |    ||| ||||  | || |  || || |||| | ||||||| || || || ||||||||||| |||||||||||||||||||| || ||||| 
gtaatggtggcgccatctttaagcatcatttagcatgttgttat--atggatctcaatgattagtgtttgagacattctgattttttgttttacacatgaatttctagAAACTTTTTAGGGGAAAGGATGGTGAGCTCTCTGTTATTGGTAGACTTGCAGCAGGTGCTTGTGCTGGCATGACGTCCACTTTT

upper sequence: AT3G51870.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S91_149V6.1 (Physcomitrella patens), 3'ss of exon 6
-ttagtcttttttgttatctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatgtgactgatgc-ttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
 | ||   || ||   || |  ||    | |   |   |   |||   |||| |||   || | |    | |   ||| | | || |   |||||  | ||||| |||||||||||| |||||||  | || ||| |  |||| |||||||| || || || |||||||||||||| |||||||||
ctgagaaattcttacgatttacatcttgattcg-attgtgtgtcgcataggatgatggatgcactcctgacgcc-ctgttacgttgtgatttttgcctacagAAATTGTTCAAAGGTGAAGATGAAGAACTTTCAATTGTCGGTAGACTTGCTGCAGGCGCATGTGCTGGCATGACCTCTACTTTG

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|19877032|gb|AU237863.1|AU237863
EST:     GAGTGTTACCTTACAGTGCGGTCCAGCTTTTGGCTTATGAGAGTTACAAG                         AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCA
genomic: GAGTGTTACCTTACAGTGCGGTCCAGCTTTTGGCTTATGAGAGTTACAAGgtgagtttgt ... ttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG
                           gactgat  putative branch site (score: 3)
                                    ttctatattttgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagtcttttttgttatctgtattgaaactgacagcattcatcgttaaggaagatttctgtattgaaaatgtgactgatgcttctatattttgtattcagAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - ttgaaac
- - - - - - - - - - - - - - - - - - - - - - - -aggaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgc